Contacts of the helix formed by residues 186 - 198 (chain A) in PDB entry 1GN2
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 ASN 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LYS 3.1 22.2 + - - +
82A ASN 2.8 18.8 + - - +
83A LEU 4.1 1.0 + - - -
84A SER* 3.4 30.4 + - - -
87A GLY* 4.7 3.1 - - - -
184A VAL 3.3 0.2 + - - -
185A VAL* 1.3 74.3 - - - +
187A TRP* 1.3 54.1 + - - +
188A ALA* 3.1 20.2 + - - +
189A ASP* 2.9 29.2 + - - +
190A VAL* 3.6 5.6 + - - +
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Residues in contact with TRP 187 (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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87A GLY* 5.5 1.0 - - - -
88A GLY* 3.6 22.6 + - - -
89A ASP 3.5 14.3 + - - -
90A LYS 4.1 9.4 - - - +
91A PRO* 3.7 37.7 - - + -
95A LEU* 4.1 2.5 - - + -
99A ILE* 4.1 9.6 - - + -
106A PHE* 3.5 34.8 - + - -
109A PHE* 4.3 6.5 - + - -
128A LEU* 5.8 0.4 - - + -
157A LEU* 4.2 13.5 - - + -
182A TRP* 3.8 24.9 + + - -
185A VAL* 3.5 25.7 + - + +
186A ASN* 1.3 70.4 + - - +
188A ALA* 1.3 61.5 + - - +
189A ASP 3.1 0.4 - - - -
190A VAL* 4.0 30.5 - - + +
191A GLN* 3.0 33.5 + - - +
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Residues in contact with ALA 188 (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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186A ASN* 2.9 12.7 + - - +
187A TRP* 1.3 76.9 - - - +
189A ASP* 1.3 59.3 + - - +
191A GLN* 4.0 8.4 - - - +
192A SER* 3.2 26.0 + - - -
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Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.7 21.8 - - - +
82A ASN* 2.8 21.8 + - - +
186A ASN* 2.9 27.1 + - - +
188A ALA* 1.3 79.8 - - - +
190A VAL* 1.3 66.8 + - - +
192A SER* 2.9 9.2 + - - -
193A ARG* 2.7 64.0 + - - +
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Residues in contact with VAL 190 (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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82A ASN* 4.3 5.8 - - + +
95A LEU* 3.4 23.1 - - + -
128A LEU* 4.7 7.2 - - + -
156A LEU* 4.1 26.5 - - + +
157A LEU* 4.0 31.2 - - + -
185A VAL* 4.6 0.9 - - + -
186A ASN 3.9 13.7 - - - +
187A TRP* 4.1 24.9 - - + +
189A ASP* 1.3 73.6 + - - +
191A GLN* 1.3 53.0 - - - +
193A ARG* 3.0 11.4 + - - +
194A TYR* 2.8 33.8 + - - +
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Residues in contact with GLN 191 (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 PRO* 3.6 4.9 - - - +
92A THR* 2.6 52.7 + - - +
95A LEU* 3.1 37.0 - - + +
187A TRP* 3.0 21.0 + - - +
188A ALA* 4.0 8.1 - - - +
190A VAL* 1.3 78.5 - - - +
192A SER* 1.3 64.3 + - - +
194A TYR* 3.3 5.2 + - - +
195A ALA* 3.1 22.7 + - - +
12G ASP* 5.7 2.0 + - - -
13G TYR* 5.8 5.1 - - - -
26G GLU* 5.7 3.6 + - - +
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Residues in contact with SER 192 (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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188A ALA 3.2 14.8 + - - -
189A ASP* 2.9 16.3 + - - -
191A GLN* 1.3 81.4 - - - +
193A ARG* 1.3 61.4 + - - +
195A ALA* 3.2 9.0 + - - +
196A ALA* 3.1 21.7 + - - +
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Residues in contact with ARG 193 (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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77A THR* 5.1 1.6 + - - +
78A ILE* 3.9 37.2 - - - +
81A LYS* 3.8 20.8 - - - +
82A ASN* 3.8 2.6 - - - +
154A VAL* 5.3 1.7 - - + +
155A PRO 4.0 10.0 + - - +
156A LEU* 3.3 37.0 - - + +
189A ASP* 2.7 50.8 + - - +
190A VAL* 3.4 4.7 - - - +
192A SER* 1.3 74.4 - - - +
194A TYR* 1.3 61.0 + - - +
196A ALA* 3.4 6.4 + - - +
197A ALA* 2.9 30.1 + - - +
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Residues in contact with TYR 194 (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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94A GLU* 4.2 22.8 + - + -
95A LEU* 3.6 33.0 - - + -
98A ALA* 3.4 31.7 - - + +
130A TRP* 4.2 18.7 - + - -
137A LEU* 4.3 7.9 - - + -
156A LEU* 3.8 25.0 - - + +
190A VAL 2.8 15.7 + - - +
191A GLN 3.6 5.4 - - - +
193A ARG* 1.3 78.2 - - - +
195A ALA* 1.3 54.1 + - + +
197A ALA* 3.2 2.0 + - + +
198A THR* 2.7 71.1 + - + +
26G GLU* 5.8 2.0 - - - -
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Residues in contact with ALA 195 (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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191A GLN 3.1 12.3 + - - +
192A SER* 3.2 13.0 + - - +
194A TYR* 1.3 81.1 - - + +
196A ALA* 1.3 61.1 + - - +
198A THR* 3.5 8.2 + - - -
199A SER* 3.4 22.2 + - - -
26G GLU* 5.2 9.2 - - - +
31G LYS* 5.6 2.3 + - - -
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Residues in contact with ALA 196 (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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192A SER* 3.1 9.7 + - - +
193A ARG* 3.9 8.7 - - - +
195A ALA* 1.3 77.2 - - - +
197A ALA* 1.3 66.4 + - - +
199A SER* 3.2 19.4 + - - +
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Residues in contact with ALA 197 (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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130A TRP* 3.7 41.5 + - + -
132A THR* 5.2 3.3 - - - +
154A VAL* 4.2 22.2 - - + +
156A LEU* 4.2 3.6 - - + -
193A ARG 2.9 19.3 + - - +
194A TYR* 3.5 5.4 - - + +
196A ALA* 1.3 79.5 - - - +
198A THR* 1.3 58.5 - - - +
199A SER 3.1 6.5 + - - -
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Residues in contact with THR 198 (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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130A TRP* 3.7 32.5 - - + +
194A TYR* 2.7 67.2 + - + +
195A ALA* 3.6 9.5 + - - -
196A ALA 3.3 0.4 - - - -
197A ALA* 1.3 72.2 - - - +
199A SER* 1.3 60.5 + - - +
31G LYS* 5.7 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
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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