Contacts of the helix formed by residues 109 - 131 (chain H) in PDB entry 3UF2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 109 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H THR 4.0 11.4 + - - +
30H SER* 3.4 21.3 - - - +
31H CYS 3.1 19.7 - - - +
32H GLN* 4.2 4.9 - - + +
33H ILE* 4.5 0.9 - - - -
108H GLU* 1.3 74.9 - - - +
110H PRO* 1.3 72.8 - - - +
111H LEU* 3.8 8.3 + - - +
112H GLN* 2.9 46.2 + - - +
113H LEU* 3.0 20.4 + - - +
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Residues in contact with PRO 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G MET* 4.0 17.3 - - + -
30G SER* 3.8 25.6 - - - +
31G CYS* 4.0 11.0 - - - -
26H GLN* 5.6 6.7 - - + +
29H THR* 4.4 9.6 - - - +
31H CYS 3.5 10.5 - - - +
33H ILE* 4.1 21.5 - - + -
108H GLU 4.3 1.8 - - - +
109H THR* 1.3 86.9 - - - +
111H LEU* 1.3 54.3 + - + +
113H LEU* 2.9 6.5 + - + +
114H LEU* 2.8 44.6 + - + +
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Residues in contact with LEU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H ILE* 3.8 29.0 - - + +
26H GLN* 3.5 33.9 - - + +
27H MET 4.7 1.8 - - - +
28H GLU* 4.1 35.4 - - + -
29H THR 4.7 9.9 - - - +
109H THR* 3.3 7.3 + - - +
110H PRO* 1.3 80.2 - - + +
112H GLN* 1.3 58.9 + - + +
114H LEU* 3.3 6.4 + - + +
115H GLU* 2.9 28.8 + - - +
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Residues in contact with GLN 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H GLN* 5.4 1.0 + - - +
108H GLU* 3.5 27.8 + - + +
109H THR* 2.9 47.7 + - - +
111H LEU* 1.3 74.8 - - + +
113H LEU* 1.3 65.1 + - - +
115H GLU* 3.4 8.2 + - - +
116H LYS* 3.3 28.1 + - - +
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Residues in contact with LEU 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G MET* 5.1 4.3 - - + -
33H ILE* 3.9 12.8 - - + -
35H PHE* 3.6 50.7 - - + -
60H ILE* 3.7 31.4 - - + -
64H THR* 3.4 33.2 - - + -
65H MET* 4.6 8.3 - - + -
108H GLU* 4.6 0.8 + - - -
109H THR 3.0 9.2 + - - +
110H PRO* 2.9 10.2 + - + +
112H GLN* 1.3 77.9 - - - +
114H LEU* 1.3 61.9 + - + +
116H LYS* 3.4 7.1 + - + +
117H VAL* 3.1 19.9 + - + +
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Residues in contact with LEU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G MET* 4.4 15.3 - - - -
19H LEU* 5.3 3.6 - - + +
22H LEU* 3.5 27.8 - - + -
23H ILE* 3.8 21.4 - - + +
26H GLN* 3.4 34.3 - - + +
65H MET* 3.7 29.2 - - + -
110H PRO* 2.8 24.9 + - + +
111H LEU* 3.6 9.4 - - - +
113H LEU* 1.3 77.0 - - + +
115H GLU* 1.3 59.5 + - - +
117H VAL* 3.2 6.2 + - + +
118H LYS* 2.9 29.5 + - - +
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Residues in contact with GLU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLN* 5.7 0.2 + - - -
23H ILE* 3.9 12.4 - - - +
111H LEU 2.9 16.8 + - - +
112H GLN* 3.7 9.4 - - - +
113H LEU 3.3 0.2 - - - -
114H LEU* 1.3 76.2 - - - +
116H LYS* 1.3 58.1 + - + +
118H LYS* 3.3 31.7 + - - +
119H ASN* 2.9 53.6 + - - +
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Residues in contact with LYS 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H PHE* 4.2 15.9 - - + -
37H PHE* 3.9 39.9 - - + -
40H GLN* 6.6 0.2 - - - -
49H TYR* 5.9 0.9 - - - -
106H PHE* 4.1 23.0 - - - -
108H GLU* 2.8 33.3 + - - +
112H GLN* 3.3 13.4 + - - +
113H LEU* 3.4 8.5 - - + +
115H GLU* 1.3 78.0 - - + +
117H VAL* 1.3 57.1 + - + +
119H ASN* 3.4 6.4 + - - +
120H VAL* 2.9 36.5 + - - +
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Residues in contact with VAL 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LEU* 4.3 15.0 - - + -
57H VAL* 4.1 22.9 - - + -
60H ILE* 4.0 28.0 - - + -
61H MET* 4.9 3.4 - - + -
65H MET* 4.0 19.3 - - + -
113H LEU* 3.1 18.7 + - + +
114H LEU* 3.2 8.5 + - - +
116H LYS* 1.3 76.3 - - + +
118H LYS* 1.3 65.4 + - - +
120H VAL* 3.4 1.6 + - - +
121H PHE* 3.2 44.8 + - + -
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Residues in contact with LYS 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H LEU 5.1 2.9 - - - +
19H LEU* 3.6 20.8 - - + +
20H GLN* 2.9 39.0 + - + +
23H ILE* 3.8 15.3 - - + -
114H LEU 2.9 16.7 + - - +
115H GLU* 3.5 34.2 + - - +
117H VAL* 1.3 76.6 - - - +
119H ASN* 1.3 71.3 + - - +
121H PHE* 3.1 4.7 + - - +
122H ASN* 2.9 44.5 + - - +
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Residues in contact with ASN 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H GLU* 2.9 41.3 + - - +
116H LYS* 3.7 6.2 - - - +
118H LYS* 1.3 82.5 - - - +
120H VAL* 1.3 55.3 + - + +
122H ASN* 3.7 6.4 - - - +
123H GLU* 2.7 49.0 + - + +
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Residues in contact with VAL 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.7 25.8 - - + -
49H TYR* 5.4 3.6 - - + -
50H LEU* 4.4 9.0 - - + +
53H ALA* 3.8 13.2 - - + -
54H PHE* 4.0 26.2 - - + +
57H VAL* 3.8 21.8 - - + -
116H LYS 2.9 21.6 + - - +
117H VAL 3.7 4.9 - - - +
118H LYS 3.2 0.4 - - - -
119H ASN* 1.3 74.9 - - + +
121H PHE* 1.3 56.8 + - + +
123H GLU* 3.8 5.4 - - - +
124H THR* 2.7 42.9 + - - +
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Residues in contact with PHE 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ILE* 3.8 19.1 - - + +
16H LEU* 3.8 19.3 - - + -
19H LEU* 3.7 14.4 - - + -
54H PHE* 4.4 16.2 - + - -
57H VAL* 3.8 14.6 - - + -
58H GLN* 4.5 1.1 - - - -
61H MET* 3.9 22.4 - - + -
80H LEU* 4.1 23.3 - - + -
83H LEU* 4.5 9.0 - - + -
84H SER* 3.8 24.7 - - - -
87H LEU* 5.1 0.2 - - + -
117H VAL* 3.2 36.0 + - + -
118H LYS 3.1 6.5 + - - +
120H VAL* 1.3 76.3 - - + +
122H ASN* 1.3 60.9 + - - +
124H THR* 3.2 6.3 + - - -
125H LYS* 2.8 30.0 + - - +
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Residues in contact with ASN 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H LEU* 3.7 38.9 + - - +
118H LYS* 2.9 49.1 + - - +
119H ASN* 3.7 6.7 - - - +
121H PHE* 1.3 76.6 - - - +
123H GLU* 1.3 64.8 + - + +
125H LYS* 3.0 2.6 + - - +
126H ASN* 2.9 39.7 + - - +
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Residues in contact with GLU 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H LEU* 3.5 31.6 - - + +
119H ASN* 2.7 38.9 + - + +
120H VAL 3.8 0.2 - - - +
122H ASN* 1.3 72.9 - - + +
124H THR* 1.3 61.6 + - - +
126H ASN* 4.0 11.1 + - - +
127H LEU* 3.3 34.3 + - - +
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Residues in contact with THR 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ILE* 3.4 20.9 - - + -
50H LEU* 4.6 7.1 - - - +
54H PHE* 4.5 11.7 - - + +
87H LEU* 4.9 4.9 - - + -
91H PHE* 4.8 7.6 - - + -
120H VAL* 2.7 30.0 + - - +
121H PHE* 3.3 7.4 - - - -
122H ASN 3.1 0.2 - - - -
123H GLU* 1.3 78.5 - - - +
125H LYS* 1.3 62.1 + - - +
127H LEU* 3.9 1.9 - - - +
128H LEU* 3.0 39.3 + - + +
135H PHE* 3.9 25.8 - - + -
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Residues in contact with LYS 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H SER 5.7 1.1 - - - +
11H ILE* 3.4 42.4 - - + +
12H GLY* 4.6 0.4 - - - -
13H SER* 4.2 23.9 + - - +
16H LEU* 3.4 26.7 - - + +
121H PHE 2.8 16.4 + - - +
122H ASN 3.0 3.8 + - - +
124H THR* 1.3 75.0 - - - +
126H ASN* 1.3 73.1 + - - +
127H LEU 3.1 0.2 + - - -
128H LEU* 3.1 5.1 + - - +
129H ASP* 3.0 47.2 + - - +
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Residues in contact with ASN 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H LEU* 5.8 0.9 - - - +
122H ASN* 2.9 33.3 + - - +
123H GLU* 4.0 12.6 + - - +
125H LYS* 1.3 83.6 + - - +
127H LEU* 1.3 64.3 + - + +
129H ASP* 3.6 11.4 - - - +
130H LYS* 3.1 38.2 + - - +
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Residues in contact with LEU 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H PRO* 6.2 1.6 - - + -
47H VAL* 5.2 4.9 - - + +
50H LEU* 3.5 30.1 - - + -
123H GLU* 3.3 17.8 + - - +
124H THR* 3.9 3.4 - - - +
125H LYS 3.1 0.8 - - - -
126H ASN* 1.3 77.1 - - + +
128H LEU* 1.3 56.3 - - - +
129H ASP 3.1 1.8 - - - -
130H LYS* 3.0 19.5 + - - +
131H ASP* 2.7 37.2 + - + +
134H ILE* 3.9 34.1 - - + -
135H PHE* 4.9 4.3 - - + -
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Residues in contact with LEU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H CYS* 3.7 26.0 - - + +
8H SER* 3.2 24.4 + - - +
11H ILE* 4.5 5.4 - - + -
87H LEU* 3.7 25.1 - - + -
90H CYS* 5.1 2.7 - - + -
91H PHE* 5.5 0.4 - - + -
124H THR* 3.0 39.0 + - + +
125H LYS* 3.1 4.7 + - - +
127H LEU* 1.3 76.6 - - - +
129H ASP* 1.3 62.0 + - - +
131H ASP 4.0 4.5 - - - +
132H TRP* 3.4 40.6 + - - +
135H PHE* 3.9 25.6 - - + -
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Residues in contact with ASP 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H SER* 3.4 27.4 + - - +
125H LYS* 3.0 49.8 + - - +
126H ASN* 3.6 12.2 - - - +
127H LEU 3.1 0.2 - - - -
128H LEU* 1.3 80.3 - - - +
130H LYS* 1.3 65.3 + - + +
132H TRP* 5.5 1.7 - - - -
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Residues in contact with LYS 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H ASN* 3.1 40.4 + - - +
127H LEU* 3.0 18.1 + - - +
129H ASP* 1.3 87.8 - - + +
131H ASP* 1.3 62.3 + - + +
132H TRP* 4.0 5.9 + - - -
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Residues in contact with ASP 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H LEU 2.7 16.6 + - - +
128H LEU* 4.0 0.3 - - - -
130H LYS* 1.3 75.5 - - + +
132H TRP* 1.3 63.7 + - - +
133H ASN* 3.4 17.5 + - - +
134H ILE* 3.1 47.8 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il