Contacts of the helix formed by residues 116 - 138 (chain B) in PDB entry 3GHG
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 GLN 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B SER 4.2 5.4 - - - +
113B SER* 2.5 35.3 + - - +
115B PHE* 1.3 78.5 - - + +
117B TYR* 1.3 76.2 + - - +
118B MET 3.1 3.6 + - - +
119B TYR* 3.5 30.0 + - + +
120B LEU* 4.0 17.5 + - - +
53C LYS* 5.9 5.4 - - - +
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 6.2 5.4 - - + -
113B SER* 3.3 33.7 + - - -
114B SER* 3.4 28.1 + - - +
116B GLN* 1.3 88.6 - - - +
118B MET* 1.3 67.5 + - + +
119B TYR 3.5 0.2 - - - -
120B LEU* 3.6 15.9 - - + +
121B LEU* 3.0 47.7 + - + +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 5.6 12.3 - - + +
90A ILE* 5.8 7.6 - - + -
114B SER 5.0 4.3 - - - +
115B PHE 4.1 9.6 - - - +
116B GLN 3.1 0.8 - - - -
117B TYR* 1.3 87.5 - - + +
119B TYR* 1.3 65.5 + - + +
121B LEU* 2.9 11.7 + - + -
122B LYS* 2.3 50.6 + - + +
57C VAL* 3.5 33.9 - - + -
60C LEU* 4.7 19.3 - - + -
61C ILE* 5.2 13.5 - - + -
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Residues in contact with TYR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE 5.2 2.5 - - - -
116B GLN* 3.5 27.1 + - + +
118B MET* 1.3 82.1 - - + +
120B LEU* 1.3 57.4 + - + +
122B LYS* 4.6 4.3 - - + -
123B ASP* 3.3 31.2 - - - +
53C LYS* 6.2 3.6 - - - -
56C GLU* 5.3 4.0 + - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 4.0 23.3 + - - +
117B TYR* 3.6 20.2 - - + +
118B MET 3.2 0.2 - - - -
119B TYR* 1.3 79.3 - - + +
121B LEU* 1.3 88.6 + - + +
123B ASP* 4.5 3.8 - - - +
124B LEU* 3.8 17.7 + - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 6.3 3.4 - - + -
91A MET* 6.1 2.9 - - + -
95A ARG* 5.4 10.1 - - - +
117B TYR* 3.0 39.1 + - + +
118B MET* 2.9 12.4 + - + -
120B LEU* 1.3 99.1 - - + +
122B LYS* 1.3 64.8 + - - +
123B ASP 3.4 0.2 - - - -
124B LEU* 3.6 19.2 + - + +
125B TRP* 3.1 22.2 + - - +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 2.3 46.2 + - + +
119B TYR* 4.6 2.9 - - + +
121B LEU* 1.3 65.7 - - - +
123B ASP* 1.3 60.6 + - - +
125B TRP* 2.8 10.1 + - - +
126B GLN* 2.6 65.4 + - + +
60C LEU* 3.4 45.9 - - + +
64C ILE* 5.0 11.4 - - + +
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 3.3 22.9 + - - +
120B LEU* 4.5 4.7 - - - +
122B LYS* 1.3 85.4 - - - +
124B LEU* 1.3 50.9 + - - +
126B GLN* 2.9 9.3 + - - +
127B LYS* 2.4 56.3 + - + +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 5.3 9.7 - - + -
120B LEU 3.8 14.2 + - - +
121B LEU* 3.6 21.6 + - + +
122B LYS 3.2 0.2 - - - -
123B ASP* 1.3 78.5 - - - +
125B TRP* 1.3 59.5 + - + +
127B LYS* 4.0 15.9 - - + +
128B ARG* 3.0 44.1 + - + +
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Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.2 51.8 - - + -
97A ASP* 5.1 0.4 - - - -
98A PHE* 3.6 26.2 - + - -
121B LEU 3.1 12.9 + - - +
122B LYS* 2.8 10.4 + - - +
124B LEU* 1.3 78.1 - - + +
126B GLN* 1.3 67.3 + - - +
127B LYS 3.2 1.7 + - - -
129B GLN* 3.1 55.7 + - + +
64C ILE* 3.8 43.1 + - + +
68C TYR* 3.4 32.1 - + + +
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Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LYS* 2.6 45.9 + - + +
123B ASP* 3.0 9.6 - - - +
125B TRP* 1.3 77.5 + - + +
127B LYS* 1.3 58.5 + - - +
129B GLN* 3.7 8.0 - - - +
130B LYS* 3.1 54.4 - - - +
64C ILE* 3.3 32.1 - - - +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 2.4 45.5 + - + +
124B LEU* 3.9 14.8 - - - +
125B TRP 3.2 0.4 - - - -
126B GLN* 1.3 74.1 - - - +
128B ARG* 1.3 59.5 + - + +
129B GLN 3.4 1.1 - - - -
130B LYS* 3.1 3.0 + - - +
131B GLN* 2.6 38.6 + - - +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.4 64.7 + - + +
101A ALA* 4.7 8.1 - - - +
102A ASN* 5.5 4.0 - - - +
124B LEU* 3.0 27.7 + - + +
127B LYS* 1.3 76.4 - - + +
129B GLN* 1.3 66.6 + - - +
131B GLN* 4.2 7.5 + - + +
132B VAL* 3.2 48.4 + - - +
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.5 20.5 - - + -
125B TRP* 3.1 51.4 + - + +
126B GLN* 3.7 10.9 - - - +
127B LYS 3.4 0.2 - - - -
128B ARG* 1.3 77.9 - - - +
130B LYS* 1.3 69.7 + - - +
132B VAL* 3.6 14.9 - - - +
133B LYS* 3.3 43.6 + - - +
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLN* 3.1 57.1 + - - +
127B LYS* 3.1 4.2 + - - +
129B GLN* 1.3 91.3 - - - +
131B GLN* 1.3 61.3 + - - +
132B VAL 3.4 0.4 - - - -
133B LYS* 3.4 43.5 - - - +
134B ASP* 4.0 9.9 + - - +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LYS 2.6 19.6 + - - +
128B ARG* 3.5 11.3 + - + +
130B LYS* 1.3 74.3 - - - +
132B VAL* 1.3 72.1 + - - +
133B LYS 3.5 0.2 - - - -
134B ASP* 4.4 1.8 - - - +
135B ASN* 3.0 46.8 + - - +
139B VAL* 5.6 2.4 - - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 4.5 8.7 - - + -
101A ALA* 5.9 4.0 - - + -
128B ARG* 3.2 43.7 - - - +
129B GLN* 3.6 13.2 - - - +
131B GLN* 1.3 88.8 - - - +
133B LYS* 1.3 60.6 + - + +
134B ASP 3.4 0.4 - - - -
135B ASN* 3.7 10.3 - - + +
136B GLU* 3.1 22.3 + - - +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLN* 3.3 36.7 + - - +
130B LYS* 3.4 41.5 - - - +
132B VAL* 1.3 81.3 - - + +
134B ASP* 1.3 64.2 + - + +
136B GLU* 3.6 11.8 - - - +
137B ASN* 3.5 20.3 - - - +
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Residues in contact with ASP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS 4.0 11.4 + - - +
131B GLN 3.9 3.4 + - - +
133B LYS* 1.3 81.2 - - + +
135B ASN* 1.3 57.2 + - - +
136B GLU 3.0 1.3 - - - -
137B ASN* 3.0 9.1 + - - +
138B VAL* 2.5 59.9 + - + +
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Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLN* 3.0 39.8 + - - +
132B VAL* 3.7 13.1 - - - +
134B ASP* 1.3 74.3 - - - +
136B GLU* 1.3 53.6 + - - +
138B VAL* 4.1 0.8 - - - +
139B VAL* 3.2 40.4 + - + +
140B ASN* 2.8 33.1 + - - +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL 3.1 15.9 + - - +
133B LYS* 3.6 14.5 - - - +
134B ASP 3.0 0.6 - - - -
135B ASN* 1.3 75.4 + - - +
137B ASN* 1.3 73.6 + - - +
140B ASN* 2.3 52.0 + - - +
75C LYS* 4.4 17.9 + - - +
76C PRO 4.3 5.5 - - - +
77C ASN* 3.4 31.9 - - - +
78C MET* 4.4 10.0 - - - +
79C ILE 5.3 2.9 - - - +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LYS 3.5 10.6 - - - +
134B ASP* 3.0 12.8 + - - +
136B GLU* 1.3 107.8 + - - +
138B VAL* 1.3 58.7 + - - +
140B ASN 3.6 8.4 - - - +
141B GLU* 4.1 24.0 + - - +
77C ASN* 5.9 3.6 - - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASP* 2.5 53.0 + - + +
135B ASN 4.1 0.2 - - - +
136B GLU 3.3 0.2 - - - -
137B ASN* 1.3 74.1 - - - +
139B VAL* 1.3 89.1 + - + +
140B ASN 3.2 5.4 + - - -
141B GLU* 4.2 3.5 + - - +
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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