Contacts of the helix formed by residues 108 - 125 (chain B) in PDB entry 3GNI
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 SER 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ARG* 3.8 2.7 - - - +
106B ALA 4.1 0.6 + - - -
107B CYS* 1.3 77.0 - - - +
109B ASN* 1.3 65.6 + - - +
110B GLU* 3.8 9.1 + - - +
111B MET* 3.3 34.5 + - - +
112B VAL* 3.1 20.8 + - - +
236B TYR* 4.4 1.4 + - - -
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Residues in contact with ASN 109 (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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227A ARG* 3.3 23.5 + - - +
231A LYS* 3.5 41.2 - - - +
273A GLU* 4.3 4.3 + - - +
108B SER* 1.3 74.1 - - - +
110B GLU* 1.3 62.5 + - - +
112B VAL* 3.1 8.6 + - - +
113B THR* 3.1 25.9 + - - -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B SER* 3.3 7.3 - - - +
109B ASN* 1.3 79.7 - - - +
111B MET* 1.3 57.6 + - - +
113B THR* 3.4 9.3 + - + -
114B PHE* 3.0 28.1 + - - +
235B LYS* 2.9 43.3 + - - +
236B TYR* 3.2 15.8 + - - +
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Residues in contact with MET 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.5 25.9 - - + -
80B GLU* 5.9 4.3 - - + -
82B LEU* 3.4 33.4 - - + -
106B ALA 4.4 2.5 - - - +
107B CYS* 3.9 13.0 - - + -
108B SER* 3.3 36.0 + - - +
109B ASN 3.3 0.8 - - - -
110B GLU* 1.3 75.8 - - - +
112B VAL* 1.3 58.9 + - - +
114B PHE* 3.6 6.0 + - - +
115B LEU* 3.1 35.2 + - - +
236B TYR* 3.5 31.9 - - + +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 5.5 2.5 - - + -
224A VAL* 5.3 9.9 - - + -
227A ARG* 4.2 20.4 - - - +
228A GLN* 5.7 2.2 - - + +
104B LEU* 4.5 19.3 - - + -
107B CYS* 3.8 16.6 - - + -
108B SER 3.1 15.7 + - - +
109B ASN* 3.1 8.5 + - - +
111B MET* 1.3 76.8 - - - +
113B THR* 1.3 57.5 + - - +
115B LEU* 3.3 8.8 + - - +
116B GLN* 3.0 50.2 + - + +
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Residues in contact with THR 113 (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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109B ASN* 3.1 14.8 + - - +
110B GLU* 3.5 13.1 - - + +
112B VAL* 1.3 74.4 - - - +
114B PHE* 1.3 64.9 + - - +
116B GLN* 3.3 14.3 + - - +
117B GLY* 3.1 20.1 + - - -
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.9 11.2 - + - -
110B GLU 3.0 17.8 + - - +
111B MET 3.6 4.5 - - - +
112B VAL 3.3 0.2 - - - -
113B THR* 1.3 78.7 - - - +
115B LEU* 1.3 61.0 + - - +
117B GLY* 3.5 8.0 + - - -
118B GLU* 3.5 10.4 + - - +
194B ARG* 4.9 10.8 - - - -
215B ARG* 3.4 56.3 - - + +
216B SER* 4.6 6.1 - - - -
235B LYS* 3.4 46.0 - - + +
236B TYR* 3.5 31.2 - + + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.9 30.7 - - + -
102B ILE* 3.8 28.3 - - + -
104B LEU* 4.1 17.7 - - + -
107B CYS* 4.0 16.4 - - - -
111B MET 3.1 26.3 + - - +
112B VAL* 3.6 6.1 - - + +
113B THR 3.2 0.2 - - - -
114B PHE* 1.3 75.8 - - - +
116B GLN* 1.3 62.2 + - - +
118B GLU* 3.4 24.1 + - - +
119B LEU* 3.5 17.3 - - - +
143B LEU* 4.3 16.8 - - + +
215B ARG* 4.2 18.6 - - - +
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 3.3 25.7 - - + -
182A SER* 3.2 36.0 + - - +
224A VAL* 4.6 0.6 - - - +
228A GLN* 3.4 24.2 + - - +
112B VAL* 3.0 32.7 + - + +
113B THR* 3.3 15.5 + - - +
115B LEU* 1.3 73.0 - - + +
117B GLY* 1.3 64.5 + - - +
119B LEU* 3.3 12.9 + - + +
120B HIS* 3.2 20.6 + - - +
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Residues in contact with GLY 117 (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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113B THR 3.1 13.6 + - - -
114B PHE* 3.8 5.8 - - - -
115B LEU 3.3 0.4 - - - -
116B GLN* 1.3 73.0 - - - +
118B GLU* 1.3 57.6 + - - +
120B HIS* 3.2 9.0 + - - +
121B VAL* 3.0 37.3 + - - +
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Residues in contact with GLU 118 (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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100B ARG* 4.1 17.8 + - - -
114B PHE 3.5 5.6 + - - +
115B LEU* 3.4 19.4 + - - +
116B GLN 3.3 0.4 - - - -
117B GLY* 1.3 74.4 - - - +
119B LEU* 1.3 61.7 + - + +
121B VAL* 3.5 3.4 + - - +
122B SER* 3.1 27.7 + - - -
133B TYR* 2.5 37.5 + - + +
145B VAL* 6.0 1.9 - - - +
214B LEU* 4.0 9.2 + - + +
215B ARG* 3.6 60.9 + - + +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 3.5 38.4 - - + -
179A ASP* 4.2 24.3 - - + +
182A SER* 5.2 0.9 - - - +
115B LEU 3.5 13.5 - - - +
116B GLN* 3.5 14.6 - - + +
117B GLY 3.2 0.6 - - - -
118B GLU* 1.3 79.6 - - + +
120B HIS* 1.3 66.4 + - - +
122B SER* 3.1 15.8 + - - -
123B LYS* 3.4 17.5 + - - +
133B TYR* 5.1 6.5 - - + -
136B THR* 3.6 23.6 - - + +
143B LEU* 4.4 7.2 - - + -
145B VAL* 3.7 26.2 - - + -
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Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.0 27.3 - - + +
145A ILE* 3.7 34.6 - - + +
148A ARG* 4.5 9.4 + - - -
179A ASP* 5.5 0.9 - - - +
183A ASP* 4.2 5.9 + - - -
116B GLN 3.2 9.6 + - - +
117B GLY* 3.2 11.2 + - - +
119B LEU* 1.3 82.5 - - - +
121B VAL* 1.3 71.4 + - + +
123B LYS* 3.4 9.5 + - - +
124B LEU* 3.4 31.9 + - + +
191B TYR* 4.8 2.8 + - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLY* 3.0 18.8 + - - +
118B GLU* 4.1 5.4 - - - +
120B HIS* 1.3 83.1 - - + +
122B SER* 1.3 61.6 + - - +
124B LEU* 3.2 18.9 + - - +
125B PHE* 3.4 43.7 + - + -
191B TYR* 3.9 28.9 - - + +
214B LEU* 5.0 6.3 - - + +
217B ASN* 4.2 22.4 - - + +
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Residues in contact with SER 122 (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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118B GLU 3.1 14.9 + - - -
119B LEU* 3.1 16.6 + - - -
121B VAL* 1.3 77.5 - - - +
123B LYS* 1.3 62.1 + - - +
125B PHE* 3.4 18.6 + - - +
133B TYR* 3.6 54.0 + - - +
214B LEU* 3.8 17.1 - - - +
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Residues in contact with LYS 123 (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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92A PHE* 3.3 21.3 - - - -
141A LEU* 4.2 20.9 - - + +
179A ASP* 3.5 31.8 + - + +
119B LEU 3.4 14.8 + - - +
120B HIS 3.4 5.6 + - - +
121B VAL 3.3 0.4 - - - -
122B SER* 1.3 84.3 + - - +
124B LEU* 1.3 59.8 + - - +
125B PHE 3.4 1.0 - - - +
133B TYR* 4.0 32.0 + - + +
134B ARG 4.8 2.8 + - - -
135B ALA* 4.8 10.1 - - - +
136B THR* 4.9 7.1 - - - +
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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
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92A PHE* 3.5 8.7 - - - -
96A LYS* 2.7 58.2 + - + -
100A GLN* 6.1 1.6 - - - +
141A LEU* 3.9 17.3 - - + -
142A ASN* 4.7 2.7 - - - +
145A ILE* 4.1 14.8 - - + -
120B HIS* 3.4 34.1 + - + +
121B VAL* 3.2 10.6 + - - +
123B LYS* 1.3 78.5 - - - +
125B PHE* 1.3 62.0 + - + +
189B MET* 6.4 0.2 - - - -
191B TYR* 3.3 29.8 - - + +
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Residues in contact with PHE 125 (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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92A PHE* 4.3 3.0 - - - -
96A LYS* 4.9 0.2 - - - -
121B VAL* 3.4 31.6 + - + +
122B SER* 3.4 15.6 + - - +
123B LYS 3.4 1.1 - - - +
124B LEU* 1.3 87.3 - - + +
126B ASN* 1.3 63.3 + - - +
130B ILE* 4.4 18.7 - - + +
185B TYR* 3.7 18.8 - + + -
186B ILE* 3.7 23.8 - - + -
189B MET* 4.0 21.5 - - + -
191B TYR* 3.8 31.2 - + + -
214B LEU* 4.2 17.5 - - + -
217B ASN* 3.5 24.5 - - - -
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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
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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