Contacts of the helix formed by residues 106 - 129 (chain H) in PDB entry 5WUA
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 LEU 106 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H VAL* 6.1 4.0 - - + -
31H LEU* 5.0 16.1 - - + +
104H LEU* 3.2 8.4 - - + +
105H HIS* 1.3 76.3 - - - +
107H TYR* 1.3 64.7 + - - +
109H PRO* 3.3 21.6 - - - +
110H ALA* 4.3 2.4 + - - +
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Residues in contact with TYR 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ILE* 6.1 0.7 - - - -
92H GLY* 4.8 20.8 - - - +
95H SER* 6.5 0.4 - - - -
96H ASP* 4.5 22.2 - - + +
103H HIS* 5.4 3.6 - - + -
104H LEU* 3.4 17.3 + - + +
105H HIS 3.2 1.2 - - - -
106H LEU* 1.3 78.8 - - - +
108H MET* 1.3 63.3 + - - +
110H ALA* 3.9 11.3 + - - +
111H GLY* 3.9 4.7 + - - -
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Residues in contact with MET 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H LEU 4.4 1.5 + - - +
105H HIS 3.5 10.8 + - - +
106H LEU 3.3 1.0 - - - -
107H TYR* 1.3 78.8 - - - +
109H PRO* 1.3 55.0 - - - +
111H GLY* 2.5 27.8 + - - +
112H MET* 3.0 12.1 + - + +
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Residues in contact with PRO 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 4.3 23.8 - - + +
32H ASN* 5.1 3.1 - - - -
34H VAL* 6.1 1.1 - - + -
35H PRO* 5.0 17.6 - - + +
105H HIS 4.2 2.7 - - - +
106H LEU* 3.3 18.0 - - - +
108H MET* 1.3 75.3 - - + +
110H ALA* 1.3 64.2 + - - +
112H MET* 3.3 8.9 + - + +
113H ALA* 3.0 20.8 + - - +
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Residues in contact with ALA 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H LEU* 5.2 2.1 - - - +
88H GLU* 4.0 33.0 - - + +
89H ILE* 4.7 5.8 - - + +
106H LEU 4.3 2.5 + - - +
107H TYR 3.9 9.1 + - - +
109H PRO* 1.3 76.9 - - - +
111H GLY* 1.3 64.5 + - - +
113H ALA* 2.8 19.3 + - - +
114H PHE* 2.9 16.2 + - - +
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Residues in contact with GLY 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ILE* 6.1 4.4 - - - +
107H TYR 3.9 2.9 + - - -
108H MET* 2.5 18.1 + - - -
110H ALA* 1.3 75.0 - - - +
112H MET* 1.3 62.6 + - - -
114H PHE* 3.2 5.7 + - - +
115H MET* 3.0 23.7 + - - +
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Residues in contact with MET 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H PRO* 5.2 11.9 - - + +
38H PHE* 5.6 2.0 - - + -
39H LEU* 5.7 10.3 - - + +
108H MET* 3.0 8.9 + - + +
109H PRO* 3.6 11.4 - - + +
111H GLY* 1.3 74.6 - - - +
113H ALA* 1.3 64.4 + - - +
115H MET* 3.2 7.1 + - - +
116H ALA* 2.9 22.2 + - - +
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Residues in contact with ALA 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PHE* 4.7 11.2 - - + -
85H LEU* 5.2 3.6 - - + -
109H PRO 3.0 11.1 + - - +
110H ALA* 2.8 19.2 + - - +
112H MET* 1.3 71.3 - - - +
114H PHE* 1.3 55.1 + - - +
116H ALA* 2.6 30.0 + - - +
117H ALA* 3.0 14.6 + - - +
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Residues in contact with PHE 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H LEU* 3.4 40.1 - - + +
86H VAL* 4.6 4.0 - - + +
110H ALA 2.9 15.5 + - - +
111H GLY* 4.0 5.2 - - - +
113H ALA* 1.3 72.7 - - - +
115H MET* 1.3 62.4 + - - +
117H ALA* 4.4 3.7 - - - +
118H ILE* 3.9 15.9 + - - +
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Residues in contact with MET 115 (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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111H GLY 3.0 13.7 + - - +
112H MET* 3.4 11.2 - - - +
114H PHE* 1.3 77.4 - - - +
116H ALA* 1.3 64.1 + - - +
118H ILE* 3.4 16.5 - - - +
119H THR* 3.7 5.5 + - - -
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Residues in contact with ALA 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PHE* 4.0 34.8 - - + +
39H LEU* 5.0 1.1 - - - +
41H PHE* 5.8 2.0 - - + -
42H ILE* 4.9 16.4 - - + +
112H MET 2.9 12.0 + - - +
113H ALA 2.6 14.3 + - - +
115H MET* 1.3 71.0 - - - +
117H ALA* 1.3 67.0 + - - +
119H THR* 2.9 18.3 + - - -
120H SER* 2.9 10.5 + - - -
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Residues in contact with ALA 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H LEU* 6.0 7.0 - - + -
82H LEU* 6.2 3.6 - - - +
113H ALA 3.0 10.2 + - - +
114H PHE* 5.1 4.0 - - - +
116H ALA* 1.3 77.6 - - - +
118H ILE* 1.3 64.5 + - - +
120H SER* 2.9 26.8 + - - -
121H VAL* 3.1 6.9 + - - +
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Residues in contact with ILE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H LEU* 6.5 0.7 - - - -
114H PHE 3.9 12.6 + - - +
115H MET* 3.4 13.9 + - - +
116H ALA 3.0 0.2 - - - -
117H ALA* 1.3 78.5 - - - +
119H THR* 1.3 64.2 + - - +
121H VAL* 3.2 14.7 + - - +
122H VAL* 3.4 7.5 + - - +
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Residues in contact with THR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ILE* 5.3 12.6 - - - -
45H PRO* 5.9 5.2 - - - -
115H MET 3.7 4.8 + - - -
116H ALA* 2.9 12.6 + - - -
118H ILE* 1.3 75.5 - - - +
120H SER* 1.3 55.8 + - - +
122H VAL* 2.6 31.8 + - - +
123H TYR* 2.9 13.7 + - - +
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Residues in contact with SER 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H PHE* 6.3 3.6 - - - -
116H ALA 2.9 6.9 + - - -
117H ALA* 2.9 27.6 + - - -
119H THR* 1.3 75.5 - - - +
121H VAL* 1.3 60.7 + - - -
123H TYR* 3.2 6.8 + - - +
124H TYR* 3.0 19.9 + - - +
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Residues in contact with VAL 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H THR* 5.0 16.8 - - - -
117H ALA 3.1 6.6 + - - +
118H ILE* 3.5 9.9 - - - +
120H SER* 1.3 77.6 - - - +
122H VAL* 1.3 62.7 + - - +
124H TYR* 3.0 14.1 + - - +
125H HIS* 2.9 19.4 + - - +
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Residues in contact with VAL 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H ILE 3.4 2.6 + - - +
119H THR* 2.6 30.2 + - - +
121H VAL* 1.3 72.7 - - - +
123H TYR* 1.3 51.9 + - - +
125H HIS* 2.6 29.9 + - + +
126H ASN* 2.9 13.8 + - - +
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Residues in contact with TYR 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H PRO* 4.6 21.3 - - + -
49H ILE* 5.7 9.0 - - + -
119H THR 2.9 9.9 + - - +
120H SER* 3.8 8.3 - - - +
122H VAL* 1.3 75.8 - - - +
124H TYR* 1.3 63.9 + - - +
126H ASN* 3.8 5.5 - - - +
127H ILE* 2.9 28.5 + - - +
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Residues in contact with TYR 124 (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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120H SER 3.0 11.4 + - - +
121H VAL* 3.0 18.0 + - - +
123H TYR* 1.3 77.2 - - - +
125H HIS* 1.3 55.9 + - - +
127H ILE* 4.5 3.6 - - - -
128H GLU* 3.1 34.6 + - + +
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Residues in contact with HIS 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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121H VAL 2.9 9.8 + - - +
122H VAL* 2.6 23.6 + - - +
124H TYR* 1.3 72.5 - - - +
126H ASN* 1.3 56.9 + - - +
127H ILE 3.1 0.2 - - - -
128H GLU* 5.5 0.2 - - - -
129H THR* 3.0 34.4 + - - +
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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
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49H ILE* 5.1 15.9 - - + -
122H VAL 2.9 11.6 + - - +
123H TYR* 3.8 5.8 - - - +
125H HIS* 1.3 75.7 - - - +
127H ILE* 1.3 56.8 + - - +
129H THR* 5.1 1.3 - - - -
130H SER* 3.2 22.6 - - - +
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Residues in contact with ILE 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H TYR 2.9 17.5 + - - +
124H TYR* 4.0 4.3 - - - +
126H ASN* 1.3 77.7 - - - +
128H GLU* 1.3 60.3 + - - +
130H SER* 2.7 24.5 + - - -
131H ASN 2.9 20.5 + - - +
133H PRO* 6.0 4.0 - - + -
136H LEU* 3.8 30.5 - - + -
137H ILE 5.3 1.3 - - - +
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Residues in contact with GLU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H LEU* 5.0 9.2 - - - +
68H PHE* 4.2 28.4 + - + +
124H TYR* 3.1 14.9 + - + +
125H HIS* 5.5 0.2 - - - -
127H ILE* 1.3 78.6 - - - +
129H THR* 1.3 56.3 + - - +
131H ASN* 2.6 28.3 + - - +
133H PRO* 5.9 4.3 - - - -
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Residues in contact with THR 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H THR 3.6 20.3 - - - +
65H TRP* 4.9 4.1 - - - +
66H LEU* 5.1 11.7 + - - +
125H HIS* 3.0 22.9 + - - +
126H ASN* 5.1 1.3 - - - -
128H GLU* 1.3 78.1 - - - +
130H SER* 1.3 57.4 + - - +
131H ASN* 3.2 1.4 + - - +
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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