Contacts of the helix formed by residues 94 - 111 (chain B) in PDB entry 3RIG
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 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 2.8 21.0 + - - +
93B HIS* 1.3 77.1 - - + +
95B PRO* 1.4 67.2 - - - +
96B SER* 4.0 8.7 - - - +
97B ARG* 3.2 58.9 + - + +
98B VAL* 3.1 18.2 + - + +
196B ASP* 4.9 4.1 + - - +
198B SER* 6.0 1.4 - - - +
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Residues in contact with PRO 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.2 44.4 - - + +
92B ALA 4.2 5.4 - - - +
93B HIS 3.8 3.8 - - - -
94B ASN* 1.4 86.1 - - - +
96B SER* 1.4 62.5 + - - +
98B VAL* 3.8 0.7 - - - +
99B TRP* 2.9 34.0 + - - +
201B VAL* 4.4 17.0 - - + -
204B LEU* 3.8 15.7 - - + -
215B LEU* 4.4 7.2 - - + -
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASN* 3.2 7.4 - - - -
95B PRO* 1.4 82.0 - - - +
97B ARG* 1.3 59.3 + - - +
99B TRP* 3.3 1.2 + - - +
100B GLU* 2.9 30.5 + - - +
184B LEU* 5.3 0.3 - - - +
197B ALA* 4.3 2.8 + - - +
198B SER* 3.6 13.3 + - - -
199B ILE* 2.8 55.5 + - - +
204B LEU* 3.7 12.4 - - - +
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Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TRP* 3.9 17.3 - - + -
80B TRP* 3.0 51.0 - - - +
85B LEU* 4.1 13.0 - - + -
94B ASN* 3.2 45.0 + - + +
96B SER* 1.3 75.2 - - - +
98B VAL* 1.3 63.9 + - + +
100B GLU* 3.2 10.3 + - - +
101B PHE* 3.0 22.2 + - - +
196B ASP* 2.8 45.1 + - - +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.7 17.0 - - + +
90B ALA* 3.5 24.0 - - + +
91B PHE* 3.5 52.9 - - + +
94B ASN* 3.1 4.2 + - + +
95B PRO 3.9 1.6 - - - +
97B ARG* 1.3 79.2 - - + +
99B TRP* 1.3 61.9 + - - +
101B PHE* 3.2 6.6 + - - +
102B TYR* 3.0 46.6 + - + -
218B PRO* 5.2 0.9 - - + -
222B TRP* 4.0 10.8 - - + -
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Residues in contact with TRP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.7 22.0 - + - -
95B PRO 2.9 20.4 + - - +
96B SER 3.3 3.1 + - - +
98B VAL* 1.3 73.1 - - - +
100B GLU* 1.3 52.7 + - - +
102B TYR* 4.1 12.1 - - + -
103B HIS* 2.7 37.5 + - - +
106B ARG* 4.5 9.6 - - - -
164B THR* 4.3 5.6 - - + -
180B ILE* 3.5 34.1 - - + -
184B LEU* 4.2 12.3 - - + -
204B LEU* 4.0 24.5 - - + -
205B PRO* 3.8 33.4 - - + +
215B LEU* 4.3 1.0 - - + +
216B LEU* 2.8 32.9 + - + -
217B ARG 3.6 15.0 - - - -
218B PRO* 3.7 25.6 - - + -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TRP* 3.8 10.5 - - + -
78B ARG* 2.9 36.3 + - - -
96B SER* 2.9 20.6 + - - +
97B ARG* 3.5 10.6 - - - +
99B TRP* 1.3 71.8 - - - +
101B PHE* 1.3 58.5 + - - +
103B HIS* 3.4 1.6 + - - +
104B TYR* 3.0 27.9 + - - +
184B LEU* 4.0 12.9 - - + +
187B LYS* 3.5 13.0 - - + +
188B GLY* 3.0 23.2 + - - +
195B GLN 4.6 1.2 - - - +
196B ASP* 3.7 4.0 - - - +
197B ALA* 2.8 45.6 + - + +
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TRP* 3.5 54.5 - + + -
82B ALA* 4.0 12.8 - - + -
85B LEU* 3.7 26.9 - - + -
97B ARG 3.0 13.1 + - - +
98B VAL* 3.2 9.4 + - - +
100B GLU* 1.3 77.7 - - - +
102B TYR* 1.3 82.3 + + - +
104B TYR* 3.3 6.1 + + - +
105B ARG* 2.9 50.1 + - + +
2002B NHE 3.5 39.3 - - + -
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU 4.6 0.2 - - - -
86B ALA* 3.2 15.9 - - - +
98B VAL* 3.0 40.4 + - + +
99B TRP* 4.1 11.9 - - + +
101B PHE* 1.3 94.4 - + - +
103B HIS* 1.3 58.0 - - - +
105B ARG* 3.6 2.4 - - + +
106B ARG* 2.9 37.3 + - - +
142B ILE* 4.3 4.0 - - + -
161B LEU* 3.5 24.2 - - + -
218B PRO* 3.6 30.5 - - + -
220B VAL* 4.0 6.4 - - + +
222B TRP* 3.0 33.5 + + - -
2002B NHE 2.8 38.3 + - - -
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Residues in contact with HIS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 2.7 19.9 + - - +
100B GLU 3.6 3.8 - - - +
102B TYR* 1.3 74.5 - - - +
104B TYR* 1.3 59.1 + - - +
106B ARG* 3.2 9.8 + - - +
107B GLU* 2.8 69.3 + - + +
179B PRO* 3.6 26.6 - - + +
180B ILE* 4.3 12.4 + - + +
184B LEU* 3.1 45.3 + - + +
186B GLY* 4.5 4.0 + - - -
187B LYS* 3.6 25.2 + - + -
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Residues in contact with TYR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TRP* 3.5 22.9 - + + +
100B GLU 3.0 11.6 + - - +
101B PHE* 3.3 12.8 - + - +
103B HIS* 1.3 78.2 - - - +
105B ARG* 1.3 70.1 + - + +
107B GLU* 3.3 4.5 + - - +
108B VAL* 2.8 65.0 + - + +
187B LYS 5.3 0.7 - - - -
188B GLY* 3.2 30.7 - - - +
189B ALA* 5.0 0.2 - - - -
190B PRO* 3.7 34.0 - - + +
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 2.9 44.4 + - + +
102B TYR* 3.6 6.3 - - - +
104B TYR* 1.3 87.2 - - + +
106B ARG* 1.3 57.7 + - - +
108B VAL* 4.8 2.2 - - - +
109B MET* 2.8 72.3 + - - +
142B ILE* 3.8 16.8 - - - +
143B ASP* 5.6 2.4 - - - +
161B LEU* 3.6 24.0 - - + +
2002B NHE 2.6 45.6 + - - +
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Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 4.5 15.2 - - - -
102B TYR* 2.9 27.1 + - - +
103B HIS* 3.2 8.2 + - - +
105B ARG* 1.3 76.2 - - - +
107B GLU* 1.3 66.2 + - - +
110B GLY* 2.9 28.6 + - - -
161B LEU* 3.1 42.9 + - + +
162B PHE* 3.7 21.4 - - + +
163B LYS 4.8 0.2 - - - +
164B THR* 5.0 2.2 - - - +
175B ASN* 2.8 47.1 + - - +
176B TYR* 3.9 2.4 - - - +
177B LYS 2.9 30.5 + - - +
180B ILE* 3.5 24.3 - - - +
218B PRO* 6.5 0.4 - - - -
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Residues in contact with GLU 107 (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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103B HIS* 2.8 53.7 + - + +
104B TYR* 3.8 5.2 - - - +
106B ARG* 1.3 80.9 + - - +
108B VAL* 1.3 67.9 + - + +
110B GLY* 4.3 0.5 - - - -
111B SER* 3.7 15.9 + - - -
177B LYS 4.6 2.1 - - - +
178B SER* 3.0 36.6 + - - -
179B PRO* 4.2 0.6 - - - +
180B ILE 5.0 0.3 + - - -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR* 2.8 58.5 + - + +
105B ARG* 4.1 3.4 - - - +
107B GLU* 1.3 72.4 - - + +
109B MET* 1.3 72.8 + - + +
111B SER* 2.9 24.0 + - - -
112B LYS* 3.6 27.4 - - - +
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Residues in contact with MET 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 2.8 50.6 + - - +
108B VAL* 1.3 88.3 - - + +
110B GLY* 1.3 58.1 + - - +
112B LYS* 2.9 45.0 + - + +
143B ASP* 3.6 37.9 - - + +
145B LEU* 4.2 14.3 - - + +
148B LYS* 6.0 0.5 - - - +
161B LEU* 3.8 16.6 - - + -
162B PHE* 4.2 5.8 - - + -
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG 2.9 20.6 + - - -
107B GLU 4.3 0.7 - - - -
109B MET* 1.3 77.9 - - - +
111B SER* 1.3 55.0 - - - +
112B LYS 3.8 0.2 + - - -
148B LYS* 4.2 14.9 + - - +
162B PHE* 3.7 17.1 - - - -
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU 3.7 9.4 + - - -
108B VAL* 2.9 17.3 + - - -
110B GLY* 1.3 74.1 - - - +
112B LYS* 1.3 68.7 + - - +
113B GLU* 3.9 7.8 + - - +
148B LYS* 5.5 0.9 - - - +
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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
------------------------------------------------------------
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