Contacts of the helix formed by residues 76 - 92 (chain R) in PDB entry 5IYB
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 GLY 76 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R PHE* 1.3 79.5 - - - +
77R VAL* 1.3 55.6 + - - +
79R ALA* 3.2 5.0 + - - +
80R LYS* 2.9 38.5 + - - +
185T ASP* 5.4 2.2 - - - -
188T PHE* 3.4 38.2 - - - +
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Residues in contact with VAL 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R PHE 3.2 5.8 - - - +
76R GLY* 1.3 76.0 - - - +
78R LEU* 1.3 56.8 + - - +
80R LYS* 3.2 22.4 + - - +
81R ILE* 2.9 41.9 + - + +
103R LEU* 5.3 5.2 - - + -
108R HIS* 3.4 40.8 - - + +
111R ILE* 3.8 23.1 - - + -
119R LEU* 5.0 7.9 - - + -
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Residues in contact with LEU 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R PHE* 3.2 17.9 + - + +
77R VAL* 1.3 76.8 - - - +
79R ALA* 1.3 58.7 + - - +
81R ILE* 3.1 21.2 + - + +
82R VAL* 2.9 34.7 + - + +
118R TRP* 6.0 0.4 - - + -
119R LEU* 3.6 27.0 - - + +
123R ALA* 3.5 29.8 - - + -
124R LEU* 3.6 39.3 - - + -
127R ASN* 6.3 0.2 - - - +
237T PRO* 5.6 5.8 - - + -
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Residues in contact with ALA 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R PHE* 3.2 8.0 + - + +
76R GLY 3.2 9.3 + - - +
78R LEU* 1.3 79.2 - - - +
80R LYS* 1.3 57.4 + - - +
82R VAL* 3.4 3.6 + - - +
83R ASN* 3.1 27.5 + - - +
188T PHE* 3.5 31.0 - - + -
220T ILE* 5.8 5.2 - - + +
235T LEU 5.2 0.7 - - - +
237T PRO* 4.2 29.8 - - + +
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Residues in contact with LYS 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R GLY 2.9 14.4 + - - +
77R VAL* 3.4 37.3 - - - +
79R ALA* 1.3 73.0 - - - +
81R ILE* 1.3 60.4 + - + +
83R ASN* 3.6 5.8 + - - +
84R TYR* 3.0 29.8 + - - +
108R HIS* 4.9 8.3 + - - -
181T GLN* 3.9 27.5 + - - +
184T LEU* 5.8 2.5 - - + -
185T ASP* 4.1 20.2 + - - +
188T PHE* 4.8 10.3 - - + -
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Residues in contact with ILE 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77R VAL* 2.9 31.7 + - + +
78R LEU* 3.1 30.5 + - + +
80R LYS* 1.3 75.6 - - + +
82R VAL* 1.3 55.4 + - + +
84R TYR* 3.3 8.1 + - - +
85R MET* 2.7 41.2 + - + +
99R LEU* 5.4 10.5 - - + -
102R ILE* 4.1 44.2 - - + -
103R LEU* 5.1 11.4 - - + -
106R THR* 5.8 4.3 - - + +
119R LEU* 5.3 6.5 - - + -
124R LEU* 5.3 7.6 - - + -
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Residues in contact with VAL 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R LEU* 2.9 28.1 + - + +
79R ALA 3.6 7.6 - - - +
81R ILE* 1.3 76.6 - - + +
83R ASN* 1.3 57.7 + - - +
85R MET* 3.2 24.4 + - + +
86R LYS* 2.9 29.8 + - + +
124R LEU* 5.3 1.6 - - + -
127R ASN* 4.4 14.6 - - - +
129R LYS* 5.2 10.5 - - + -
141R PRO 5.9 0.9 - - - +
237T PRO* 4.1 35.9 - - + +
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Residues in contact with ASN 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R ALA 3.1 17.3 + - - +
80R LYS* 3.9 6.1 - - - +
82R VAL* 1.3 73.6 - - - +
84R TYR* 1.3 64.2 - - - +
86R LYS* 3.3 33.4 + - - +
87R THR* 2.9 32.5 + - - -
219T GLU* 3.6 22.3 + - - +
220T ILE* 4.8 14.3 - - + +
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Residues in contact with TYR 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R LYS 3.0 19.3 + - - +
81R ILE* 3.4 6.7 - - - +
83R ASN* 1.3 75.8 - - - +
85R MET* 1.3 55.6 + - + +
87R THR* 3.1 10.2 + - + -
88R ARG* 2.4 90.9 + - + +
91R ARG* 5.4 6.5 - - - -
97R LEU* 6.4 2.0 - - + -
102R ILE* 4.7 17.5 - - + -
105R GLU* 3.1 20.2 + - + +
106R THR* 4.2 29.2 - - + -
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Residues in contact with MET 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R ILE* 2.7 23.4 + - + +
82R VAL* 3.2 31.2 + - + +
84R TYR* 1.3 78.2 - - + +
86R LYS* 1.3 56.8 + - - +
88R ARG* 4.4 1.6 - - - -
89R HIS* 3.0 25.3 + - - +
97R LEU* 5.7 5.2 - - + -
102R ILE* 5.3 14.6 - - + -
124R LEU* 5.5 4.0 - - + -
127R ASN* 5.3 5.6 - - - +
129R LYS* 5.7 1.6 - - + -
130R ILE* 4.1 19.5 - - + -
137R TYR* 6.2 2.7 - - - -
140R LYS* 3.2 62.3 - - + +
141R PRO* 4.5 6.5 - - + +
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Residues in contact with LYS 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R VAL* 2.9 18.0 + - + +
83R ASN* 3.3 31.8 + - - +
85R MET* 1.3 73.3 - - - +
87R THR* 1.3 60.6 + - - +
89R HIS* 3.3 3.8 + - - +
90R GLN* 2.9 29.3 + - + +
141R PRO* 4.2 17.9 - - + +
172R GLU* 3.9 39.6 + - + +
219T GLU* 4.6 17.8 + - - +
220T ILE* 5.9 0.4 - - - +
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Residues in contact with THR 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R ASN* 2.9 22.1 + - - -
84R TYR* 3.1 14.0 + - + -
86R LYS* 1.3 79.5 - - - +
88R ARG* 1.3 59.4 + - + +
90R GLN* 3.2 16.9 + - - +
91R ARG* 2.9 65.2 + - + +
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Residues in contact with ARG 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R TYR* 2.4 83.1 + - + +
85R MET* 4.4 1.1 - - - -
87R THR* 1.3 73.0 - - - +
89R HIS* 1.3 59.0 + - - +
91R ARG* 3.5 25.7 + - - +
92R GLY 3.2 5.4 + - - -
93R ASP* 2.7 65.2 + - - +
95R HIS* 4.1 12.2 - - - -
97R LEU* 6.1 2.4 - - - +
105R GLU* 2.4 28.2 + - - -
140R LYS* 3.3 20.9 - - - +
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Residues in contact with HIS 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R MET 3.0 18.1 + - - +
86R LYS 3.5 4.7 - - - +
87R THR 3.3 0.2 - - - -
88R ARG* 1.3 73.2 - - - +
90R GLN* 1.3 67.0 + - - +
92R GLY* 3.1 11.8 + - - -
93R ASP 4.6 2.9 - - - +
94R THR* 3.6 26.8 - - + +
139R PHE* 5.5 2.7 - - - -
140R LYS* 3.5 20.7 - - + +
141R PRO* 3.3 36.9 - - + +
142R LYS* 5.6 1.1 - - - -
144R ASN* 3.3 28.5 + - + -
146R ARG* 3.5 21.9 + - + -
172R GLU 4.6 7.2 - - - -
173R GLU* 4.0 16.4 + - - -
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Residues in contact with GLN 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R LYS* 2.9 15.8 + - + +
87R THR* 3.4 22.1 - - - +
89R HIS* 1.3 78.9 - - - +
91R ARG* 1.3 61.6 + - - +
92R GLY* 3.2 1.4 + - - -
146R ARG* 4.8 0.3 + - - -
171R ILE* 3.9 19.6 + - - +
172R GLU* 4.0 22.1 + - + +
173R GLU 4.6 2.9 - - - -
174R ALA* 3.5 33.7 + - - +
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Residues in contact with ARG 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R TYR* 5.4 5.9 - - - -
87R THR* 2.9 43.1 + - + +
88R ARG* 3.7 29.0 - - - +
89R HIS 3.3 0.2 - - - -
90R GLN* 1.3 79.2 - - + +
92R GLY* 1.3 57.8 + - - +
93R ASP* 3.8 9.1 - - - +
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Residues in contact with GLY 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R ARG 3.2 0.8 + - - -
89R HIS 3.1 11.1 + - - -
90R GLN 3.1 0.2 - - - -
91R ARG* 1.3 80.3 - - - +
93R ASP* 1.3 63.3 + - - +
94R THR* 2.9 18.2 + - - +
146R ARG* 3.6 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
------------------------------------------------------------
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