Contacts of the helix formed by residues 45 - 64 (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 ASP 45 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 3.8 2.9 - - + +
44H LYS* 1.3 77.0 - - - +
46H PRO* 1.3 72.0 - - - +
47H VAL* 3.4 6.8 + - - +
48H CYS* 2.9 31.6 + - + +
49H TYR* 2.9 30.8 + - - +
137H LYS* 2.8 31.9 + - - -
142H SER* 3.8 18.4 + - - +
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Residues in contact with PRO 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LYS 3.1 8.9 - - - +
45H ASP* 1.3 92.3 - - - +
47H VAL* 1.3 64.6 + - + +
49H TYR* 3.3 8.6 + - + +
50H LEU* 3.2 27.0 + - - +
127H LEU* 6.2 2.0 - - + -
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Residues in contact with VAL 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H ASP* 3.4 8.9 + - - +
46H PRO* 1.3 82.1 - - + +
48H CYS* 1.3 63.6 + - - +
50H LEU* 3.2 11.7 + - - +
51H LYS* 3.1 23.7 + - + +
127H LEU* 5.2 3.6 - - + -
134H ILE* 3.5 47.3 - - + +
135H PHE* 3.8 12.7 - - + -
137H LYS* 3.7 31.6 - - + +
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Residues in contact with CYS 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 3.6 10.3 - - + +
45H ASP* 2.9 30.3 + - + +
46H PRO 3.4 0.2 - - - -
47H VAL* 1.3 76.6 - - - +
49H TYR* 1.3 65.8 + - - +
51H LYS* 3.6 3.2 - - - +
52H LYS* 3.0 20.1 + - - +
137H LYS* 3.9 8.1 - - - -
139H CYS* 2.0 59.5 - - + -
142H SER* 3.6 15.3 - - - -
143H PHE* 3.8 9.7 - - + -
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Residues in contact with TYR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.8 19.1 - + - -
38H VAL* 3.5 33.4 + - + +
40H GLN* 3.4 44.4 + - + +
43H LEU* 3.6 26.0 - - + +
44H LYS 5.0 1.1 - - - +
45H ASP 2.9 19.7 + - - +
46H PRO* 3.4 9.2 - - + +
48H CYS* 1.3 77.7 - - - +
50H LEU* 1.3 71.6 + - + +
52H LYS* 3.9 1.2 - - - +
53H ALA* 2.8 43.3 + - + +
116H LYS* 5.9 0.5 - - - -
120H VAL* 5.4 3.4 - - + -
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Residues in contact with LEU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H PRO 3.2 12.5 + - - +
47H VAL* 3.2 8.1 + - - +
49H TYR* 1.3 91.8 - - + +
51H LYS* 1.3 60.2 + - - +
53H ALA* 4.1 2.7 - - + -
54H PHE* 2.8 32.9 + - - +
91H PHE* 4.8 0.4 - - - -
120H VAL* 4.4 18.7 - - + +
123H GLU* 3.5 43.3 - - + +
124H THR* 4.4 4.1 + - - +
127H LEU* 3.5 31.9 - - + -
135H PHE* 3.9 20.2 - - + -
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Residues in contact with LYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL* 3.1 17.0 + - + +
48H CYS* 3.6 8.3 - - - +
49H TYR 3.3 0.2 - - - -
50H LEU* 1.3 78.7 - - - +
52H LYS* 1.3 63.6 + - - +
54H PHE* 3.7 2.6 - - - +
55H LEU* 3.4 25.1 + - + +
91H PHE* 4.1 22.4 - - + -
92H THR* 3.3 17.7 + - - -
94H ASP* 3.2 19.4 + - - -
96H GLU* 5.6 3.8 - - - -
135H PHE* 3.2 43.9 + - + +
137H LYS 3.0 23.0 + - - +
139H CYS* 3.6 21.3 - - - -
143H PHE* 4.7 5.2 - - + -
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Residues in contact with LYS 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H VAL* 3.6 16.2 - - + -
43H LEU* 3.9 9.6 - - + -
48H CYS 3.0 13.4 + - - +
49H TYR 3.9 0.9 - - - +
51H LYS* 1.3 76.5 - - - +
53H ALA* 1.3 63.0 + - - +
55H LEU* 3.2 10.5 + - + +
56H LEU* 3.1 35.4 + - + +
96H GLU* 4.2 23.0 + - + +
101H ALA* 2.6 46.9 + - - +
102H CYS* 4.4 5.2 - - + -
103H VAL* 3.9 10.9 - - + +
143H PHE* 3.4 40.1 - - + -
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 4.0 9.3 - - + -
38H VAL* 3.4 16.9 - - + +
49H TYR* 2.8 32.1 + - + +
50H LEU* 3.8 6.7 - - + +
52H LYS* 1.3 73.3 - - - +
54H PHE* 1.3 52.6 + - - +
56H LEU* 3.1 4.8 + - - +
57H VAL* 2.7 40.4 + - - +
120H VAL* 3.8 24.0 - - + -
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Residues in contact with PHE 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H LEU 2.8 22.9 + - - +
51H LYS 3.7 4.0 - - - +
52H LYS 3.2 0.2 - - - -
53H ALA* 1.3 72.8 - - - +
55H LEU* 1.3 73.6 + - + +
57H VAL* 3.1 9.9 + - - +
58H GLN* 3.2 48.4 + - + -
84H SER* 3.7 26.0 - - - -
87H LEU* 3.8 33.9 - - + -
88H LYS* 4.5 12.3 - - + -
91H PHE* 4.1 32.8 - + + -
120H VAL* 4.0 15.0 - - + +
121H PHE* 4.4 11.7 - + - -
124H THR* 4.5 15.3 - - + +
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU* 4.5 12.2 - - - +
63C ASP* 5.2 0.5 - - - +
51H LYS* 3.5 16.8 - - + +
52H LYS* 3.2 11.3 + - + +
54H PHE* 1.3 89.3 - - + +
56H LEU* 1.3 60.6 + - + +
58H GLN* 3.1 28.4 + - + +
59H ASP* 3.4 10.5 + - - +
88H LYS* 5.1 10.3 - - + -
91H PHE* 5.8 7.9 - - + -
93H LYS* 4.7 16.4 - - - +
96H GLU* 3.4 42.4 - - + +
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Residues in contact with LEU 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLU* 4.6 18.3 - - + +
37H PHE* 3.9 12.6 - - + -
38H VAL* 3.3 43.7 - - + +
52H LYS* 3.1 22.5 + - + +
53H ALA 3.5 6.1 - - - +
55H LEU* 1.3 75.8 - - + +
57H VAL* 1.3 59.8 + - - +
59H ASP* 3.2 19.2 + - + +
60H ILE* 2.9 31.3 + - - +
103H VAL* 3.8 29.6 - - + -
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Residues in contact with VAL 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.9 11.4 - - + -
53H ALA 2.7 20.5 + - - +
54H PHE* 3.1 10.3 + - + +
56H LEU* 1.3 69.3 - - - +
58H GLN* 1.3 63.6 + - - +
60H ILE* 3.4 7.4 - - - +
61H MET* 2.8 39.6 + - + +
117H VAL* 4.1 19.3 - - + -
120H VAL* 3.8 31.2 - - + -
121H PHE* 3.8 33.4 - - + -
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Residues in contact with GLN 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU* 3.4 32.1 - - + +
54H PHE* 3.2 43.5 + - + +
55H LEU* 3.1 13.9 + - + +
57H VAL* 1.3 82.2 - - - +
59H ASP* 1.3 61.9 + - - +
61H MET* 3.2 22.5 + - - +
62H GLU* 3.2 23.0 + - - +
81H GLN* 4.5 7.1 + - - +
84H SER* 2.9 41.9 + - - +
88H LYS* 6.2 1.1 - - + -
121H PHE* 4.5 0.6 - - - -
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Residues in contact with ASP 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASP* 4.5 7.8 - - - +
62C GLU* 3.9 10.5 - - - +
63C ASP* 2.9 40.1 - - - +
55H LEU 3.8 10.9 - - - +
56H LEU* 3.2 21.9 + - + +
58H GLN* 1.3 75.8 - - - +
60H ILE* 1.3 55.0 + - + +
62H GLU* 4.5 3.6 - - - -
63H ASP* 2.8 51.2 + - - +
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Residues in contact with ILE 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H PHE* 4.1 9.6 - - + -
36H GLU 3.7 13.9 - - - +
37H PHE* 3.4 38.1 - - + -
56H LEU 2.9 16.0 + - - +
57H VAL* 3.1 13.0 + - + +
59H ASP* 1.3 77.5 - - + +
61H MET* 1.3 57.7 + - - +
64H THR* 3.0 30.5 + - - +
65H MET* 3.0 30.1 + - + -
113H LEU* 3.7 37.5 - - + -
117H VAL* 4.0 7.6 - - + -
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Residues in contact with MET 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LYS* 5.9 0.2 + - - -
57H VAL* 2.8 24.9 + - + +
58H GLN* 3.2 39.9 - - - +
59H ASP 3.4 0.2 - - - -
60H ILE* 1.3 73.9 - - - +
62H GLU* 1.3 58.6 + - - +
65H MET* 2.9 45.2 - - + +
77H ILE* 4.1 14.2 - - + +
80H LEU* 3.6 31.6 - - - +
81H GLN* 3.7 30.7 + - + +
84H SER* 3.8 11.0 - - - +
117H VAL* 4.9 1.8 - - + -
121H PHE* 3.9 15.7 - - + -
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Residues in contact with GLU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 4.9 0.7 - - - +
58C GLN* 2.5 41.1 - - + +
59C ASP* 3.8 10.5 - - - +
85C LEU* 4.5 3.3 - - - +
88C LYS* 3.5 23.6 + - - +
98C HIS* 3.5 15.0 + - + -
58H GLN 3.2 16.7 + - - +
59H ASP* 3.7 5.8 - - - +
60H ILE 3.1 0.2 - - - -
61H MET* 1.3 80.0 - - - +
63H ASP* 1.3 73.0 + - - +
65H MET 5.0 0.2 - - - -
66H ARG* 4.2 11.4 - - - +
81H GLN* 3.3 20.5 + - - +
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Residues in contact with ASP 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASP* 2.7 33.8 - - - +
98C HIS* 2.8 56.2 + - + +
29G THR* 4.6 1.0 - - - +
59H ASP* 2.8 33.7 + - - +
62H GLU* 1.3 73.7 - - - +
64H THR* 1.3 63.2 + - - +
66H ARG* 3.5 12.9 + - - -
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Residues in contact with THR 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G MET* 4.5 2.8 - - + +
29G THR* 2.6 43.1 + - + -
33H ILE* 3.9 16.2 - - + -
34H THR 4.3 9.5 + - - +
35H PHE* 4.1 15.1 - - + +
60H ILE* 3.0 17.8 + - - +
63H ASP* 1.3 84.3 - - - +
65H MET* 1.3 62.3 + - + +
66H ARG 3.7 0.2 - - - -
113H LEU* 3.4 33.0 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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