Contacts of the helix formed by residues 183 - 196 (chain A) in PDB entry 2GOJ
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS* 5.9 2.9 - - - +
78A ASP 3.6 13.8 - - - +
79A SER 2.9 16.5 + - - +
80A MET 3.5 23.7 - - - +
81A GLY* 5.0 0.5 - - - -
84A CYS* 4.0 16.8 - - - -
154A LEU* 3.7 8.5 - - - +
181A LEU 3.3 0.2 + - - -
182A VAL* 1.3 71.9 - - - +
184A TRP* 1.3 61.4 + - - +
185A ASN* 3.1 33.1 + - - +
186A PHE* 3.2 13.9 + - - +
187A ALA 3.3 13.9 + - - -
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Residues in contact with TRP 184 (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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84A CYS* 5.3 1.2 - - + +
85A GLY 3.7 14.4 + - - -
86A GLY 3.2 18.9 + - - -
87A GLU 3.5 15.5 - - - -
88A PRO* 3.5 16.8 - - + -
89A HIS* 3.8 24.9 - + + +
92A ILE* 3.8 21.7 - - + +
96A ILE* 3.8 25.1 - - + -
103A PHE* 3.5 37.9 - + - -
106A PHE* 4.4 7.6 - + - -
125A LEU* 5.0 1.6 - - + -
154A LEU* 3.8 18.2 - - + -
179A TRP* 4.8 3.6 - + - -
182A VAL* 3.5 29.3 + - + +
183A ASN* 1.3 70.2 - - - +
185A ASN* 1.3 61.2 + - - +
186A PHE 3.3 0.2 - - - -
187A ALA* 3.3 9.7 + - + +
188A ASN* 2.9 34.0 + - - -
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Residues in contact with ASN 185 (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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84A CYS* 5.0 6.8 - - - -
89A HIS* 2.7 37.6 + - - -
183A ASN* 3.1 14.8 + - - +
184A TRP* 1.3 77.8 + - - +
186A PHE* 1.3 56.8 + - - +
188A ASN* 3.4 7.7 + - - +
189A GLU* 3.1 27.0 + - - +
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Residues in contact with PHE 186 (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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8A LYS* 6.0 3.1 - - - -
75A PHE* 3.5 44.2 - + - -
78A ASP* 3.2 52.3 - - + +
79A SER* 3.6 11.9 - - - -
153A ILE 4.1 2.9 - - - -
154A LEU* 4.4 0.4 - - + -
183A ASN* 3.2 14.8 - - - +
185A ASN* 1.3 76.1 - - - +
187A ALA* 1.3 64.8 + - - +
189A GLU* 3.3 26.2 + - - +
190A ASN* 3.0 59.9 + - - -
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Residues in contact with ALA 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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92A ILE* 4.1 16.4 - - + -
153A ILE* 3.6 32.7 - - + +
154A LEU* 3.9 18.5 - - + +
183A ASN 3.3 3.2 + - - -
184A TRP* 3.3 19.9 + - + +
186A PHE* 1.3 79.2 - - - +
188A ASN* 1.3 57.1 + - - +
190A ASN 3.3 0.3 + - - -
191A LEU* 2.8 30.4 + - - +
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Residues in contact with ASN 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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89A HIS* 3.0 38.5 + - - -
90A GLY* 4.2 3.0 - - - -
91A GLU* 3.4 11.6 + - + +
92A ILE* 2.8 33.3 + - - +
184A TRP 2.9 21.7 + - - +
185A ASN* 3.7 7.4 - - - +
186A PHE 3.3 0.2 - - - -
187A ALA* 1.3 72.3 - - - +
189A GLU* 1.3 65.8 + - - +
191A LEU* 3.3 4.8 + - - +
192A LYS* 3.0 26.2 + - - +
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Residues in contact with GLU 189 (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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185A ASN 3.1 13.3 + - - +
186A PHE* 3.4 34.6 - - - +
188A ASN* 1.3 76.9 - - - +
190A ASN* 1.3 60.9 + - - +
192A LYS* 3.5 6.4 + - - +
193A LYS* 3.2 44.4 + - + +
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Residues in contact with ASN 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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75A PHE* 3.4 9.4 - - - -
151A ILE* 4.9 2.1 - - + +
152A PRO 3.6 19.3 - - - +
153A ILE* 3.0 30.1 + - - +
186A PHE* 3.0 50.3 + - - +
187A ALA 3.7 3.6 - - - +
189A GLU* 1.3 76.2 - - - +
191A LEU* 1.3 62.0 + - - +
193A LYS* 3.4 23.0 + - - +
194A ALA* 2.8 30.5 + - - +
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Residues in contact with LEU 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 GLU* 3.9 19.3 - - + +
92A ILE* 3.9 41.5 - - + +
95A LYS* 4.2 15.3 - - + -
127A LEU* 4.5 16.8 - - + -
133A LEU* 4.7 3.1 - - + -
153A ILE* 3.8 12.7 - - + +
187A ALA 2.8 17.1 + - - +
188A ASN* 3.3 7.4 + - - +
190A ASN* 1.3 76.4 - - - +
192A LYS* 1.3 56.8 + - - +
194A ALA* 3.1 2.0 + - - +
195A MET* 3.0 65.2 + - + +
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Residues in contact with LYS 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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91A GLU* 5.7 7.0 - - - +
188A ASN 3.0 16.8 + - - +
189A GLU* 3.8 6.1 - - - +
191A LEU* 1.3 77.4 - - - +
193A LYS* 1.3 63.2 + - + +
195A MET* 3.3 6.0 + - - +
196A LYS* 3.2 27.4 + - + +
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Residues in contact with LYS 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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151A ILE* 5.7 1.6 - - + -
186A PHE* 6.4 0.2 - - - -
189A GLU* 3.2 33.6 + - + +
190A ASN* 3.7 23.4 + - - +
192A LYS* 1.3 79.4 - - + +
194A ALA* 1.3 62.6 + - - +
196A LYS* 3.1 52.9 - - - +
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Residues in contact with ALA 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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127A LEU* 3.7 27.8 - - + +
131A ASN* 5.0 0.9 - - - +
151A ILE* 3.7 43.6 - - + +
153A ILE* 4.4 2.0 - - + -
190A ASN 2.8 18.8 + - - +
191A LEU* 3.1 8.7 + - - +
193A LYS* 1.3 77.5 - - - +
195A MET* 1.3 60.6 + - - +
196A LYS 3.7 4.3 + - - +
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Residues in contact with MET 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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95A LYS* 3.4 36.1 - - + -
127A LEU* 4.0 5.8 - - + -
131A ASN* 3.1 40.2 - - - +
191A LEU* 3.0 39.5 + - + +
192A LYS* 3.8 5.4 - - - +
193A LYS 3.3 0.2 - - - -
194A ALA* 1.3 76.9 - - - +
196A LYS* 1.3 61.1 + - - +
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Residues in contact with LYS 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 LYS* 3.2 12.6 + - + +
193A LYS* 3.1 57.5 - - - +
194A ALA 4.2 4.3 - - - +
195A MET* 1.3 80.9 - - - +
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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