Contacts of the helix formed by residues 102 - 120 (chain A) in PDB entry 2WMH
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A VAL 5.2 2.9 + - - -
93A LYS* 4.3 11.1 + - + +
100A ARG* 3.2 42.6 + - - +
101A ASP* 1.3 83.2 + - - +
103A LYS* 1.3 66.2 + - - +
104A GLU* 3.3 16.3 + - - +
105A LEU* 2.8 26.3 + - - +
106A ARG* 3.1 25.2 + - - +
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A THR* 1.3 74.9 - - - +
104A GLU* 1.3 73.7 + - - +
106A ARG* 3.5 7.5 + - - +
107A GLU* 3.1 54.8 + - + +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL* 3.8 15.9 - - + +
93A LYS* 6.4 1.3 - - + -
102A THR* 3.2 17.2 + - - +
103A LYS* 1.3 93.6 + - - +
105A LEU* 1.3 65.7 + - - +
107A GLU* 3.5 14.0 + - - +
108A TRP* 3.1 23.0 + - - +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO* 3.3 38.4 - - + -
91A VAL* 4.1 14.5 - - + +
92A CYS* 4.3 8.7 - - - +
99A PRO* 3.7 19.3 - - + +
100A ARG 3.4 21.8 - - - +
101A ASP* 4.2 1.1 - - - -
102A THR* 2.8 23.9 + - - +
104A GLU* 1.3 78.3 - - - +
106A ARG* 1.3 62.6 + - + +
108A TRP* 3.2 4.4 + - + +
109A TYR* 3.0 48.4 + - + +
136A VAL* 4.2 12.3 - - + -
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP* 2.9 37.8 + - - +
102A THR 3.1 15.9 + - - +
103A LYS* 3.8 6.1 - - - +
105A LEU* 1.3 74.5 - - - +
107A GLU* 1.3 58.8 + - + +
109A TYR* 3.2 9.6 + - - +
110A VAL* 2.9 37.4 + - + +
136A VAL* 4.5 7.1 - - + +
137A PRO* 3.3 26.2 - - - +
140A TRP* 3.6 41.3 - - + +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 3.1 53.0 + - + +
104A GLU* 3.8 17.2 - - - +
105A LEU 3.2 0.2 - - - -
106A ARG* 1.3 76.5 - - + +
108A TRP* 1.3 56.9 + - - +
110A VAL* 3.5 5.5 + - - +
111A LYS* 2.9 30.8 + - - +
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Residues in contact with TRP 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU 5.0 0.4 - - - -
54A GLY* 3.5 22.4 - - - -
55A ASN 4.7 0.2 - - - -
60A GLY* 2.9 26.2 + - - -
61A LEU* 3.9 11.4 - - + -
86A LEU* 3.9 25.8 - - + -
87A HIS 3.5 18.6 - - - -
88A PRO* 3.6 23.6 - - + -
91A VAL* 3.4 29.9 - - + +
104A GLU 3.1 17.5 + - - +
105A LEU 3.6 3.8 - - - +
106A ARG 3.2 0.2 - - - -
107A GLU* 1.3 76.6 - - - +
109A TYR* 1.3 89.5 + + - +
111A LYS* 3.3 10.4 + - + +
112A MET* 3.0 53.0 + - + +
125A LEU* 5.4 0.2 - - + -
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Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU 4.8 0.4 - - - -
88A PRO* 3.8 9.2 - - + +
99A PRO* 3.9 2.4 - - - +
105A LEU* 3.0 52.3 + - + +
106A ARG* 3.2 6.7 + - - +
108A TRP* 1.3 101.6 - + - +
110A VAL* 1.3 52.5 + - - +
112A MET* 3.3 2.9 + - - +
113A LEU* 2.8 40.7 + - + +
125A LEU* 3.8 30.5 - - + +
126A VAL 2.8 28.9 + - - -
127A ILE* 3.5 18.2 - - + +
136A VAL* 3.9 13.4 - - + +
140A TRP* 3.4 33.7 - + + -
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 2.9 22.6 + - + +
107A GLU* 3.9 5.4 - - - +
109A TYR* 1.3 71.6 - - - +
111A LYS* 1.3 65.2 + - - +
113A LEU* 3.2 8.2 + - + +
114A GLU* 2.9 30.3 + - + +
140A TRP* 4.3 12.3 - - + +
144A GLN* 4.1 21.3 - - - +
148A TYR* 3.8 16.4 - - - +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLY 4.9 3.2 + - - -
59A ASN* 3.5 31.8 + - - +
60A GLY* 4.4 4.4 - - - +
107A GLU 2.9 22.7 + - - +
108A TRP* 3.6 11.2 - - + +
110A VAL* 1.3 72.1 - - - +
112A MET* 1.3 79.4 + - + +
114A GLU* 3.5 7.5 + - - +
115A GLU* 3.1 27.8 + - + +
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Residues in contact with MET 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN 4.1 9.0 - - - +
60A GLY* 3.6 15.9 - - - +
61A LEU* 3.8 22.2 - - + -
67A LEU* 3.6 17.2 - - + +
86A LEU* 3.7 24.9 - - + +
108A TRP* 3.0 63.9 + - + +
109A TYR* 3.8 4.0 - - - +
111A LYS* 1.3 88.3 - - + +
113A LEU* 1.3 60.1 + - - +
115A GLU* 3.4 12.6 + - - +
116A ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TYR* 2.8 30.5 + - + +
110A VAL* 3.7 5.6 - - - +
112A MET* 1.3 70.8 - - - +
114A GLU* 1.3 58.4 + - - +
116A ALA* 3.8 3.2 - - - +
117A GLN* 2.9 32.7 + - - +
123A VAL* 4.0 16.4 - - + -
125A LEU* 4.1 21.8 - - + -
140A TRP* 5.1 0.2 - - + -
144A GLN* 4.2 18.6 - - + +
148A TYR* 3.8 40.7 - - + -
150A VAL* 4.2 2.8 - - + +
151A LEU* 3.9 37.0 - - + -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL* 2.9 27.5 + - + +
111A LYS* 3.6 7.2 - - - +
112A MET 3.3 0.2 - - - -
113A LEU* 1.3 76.1 - - - +
115A GLU* 1.3 60.9 + - - +
117A GLN* 3.5 2.9 + - - +
118A SER* 2.9 30.8 + - - -
147A LYS* 4.1 12.3 + - - -
148A TYR* 2.6 32.0 + - - +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 5.2 2.9 - - - +
66A THR* 5.9 0.5 - - - -
67A LEU* 3.6 31.9 + - + +
68A LYS* 5.0 2.3 + - - +
111A LYS* 3.1 19.0 + - + +
112A MET* 3.5 17.6 - - - +
114A GLU* 1.3 74.4 - - - +
116A ALA* 1.3 66.2 + - - +
118A SER* 3.3 8.7 + - - -
119A LEU* 3.2 45.4 + - - +
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.9 9.3 - - + +
112A MET 2.9 18.1 + - - +
113A LEU 3.9 2.9 - - - +
115A GLU* 1.3 76.2 - - - +
117A GLN* 1.3 58.5 + - - +
119A LEU 3.2 1.2 + - - -
120A ASN 2.8 24.4 + - - -
121A ILE* 2.9 38.5 + - + +
123A VAL* 3.6 23.3 - - + -
150A VAL* 3.8 8.5 - - + +
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU 2.9 19.0 + - - +
114A GLU* 3.8 4.7 - - - +
116A ALA* 1.3 76.3 - - - +
118A SER* 1.3 62.6 + - - +
120A ASN* 3.2 28.0 + - - +
147A LYS 5.0 2.7 - - - +
148A TYR* 3.3 21.3 - - + -
149A SER* 3.0 44.2 + - - +
150A VAL* 3.2 24.6 + - + +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 2.9 20.1 + - - -
115A GLU* 3.5 7.4 - - - -
117A GLN* 1.3 78.3 - - - +
119A LEU* 1.3 65.6 + - - +
120A ASN* 4.6 5.5 - - - +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 5.1 0.2 - - + -
68A LYS* 3.8 48.5 - - + +
71A TRP* 4.9 4.7 + - - -
115A GLU* 3.2 30.8 + - - +
116A ALA 3.2 0.2 + - - -
118A SER* 1.3 83.8 - - - +
120A ASN* 1.3 70.7 + - - +
121A ILE* 3.3 31.6 + - + +
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TRP* 4.4 6.9 + - - -
116A ALA 2.8 5.9 + - - -
117A GLN* 3.2 24.8 + - - +
118A SER 4.6 4.8 - - - +
119A LEU* 1.3 80.4 - - - +
121A ILE* 1.3 59.6 + - - +
122A PRO* 3.6 9.4 - - - +
149A SER* 5.7 0.2 + - - -
150A VAL* 4.0 10.3 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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