Contacts of the strand formed by residues 78 - 87 (chain B) in PDB entry 4IHB
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 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B TYR* 2.7 45.2 + - - +
70B LYS* 3.6 13.2 - - + +
71B ASP 3.5 5.6 - - - +
72B HIS* 3.6 13.7 + - - -
73B GLU 4.2 0.3 + - - -
74B THR* 3.0 17.2 + - - -
75B MET 4.8 2.9 - - - +
77B ARG* 1.3 87.8 - - - +
79B ARG* 1.3 62.7 + - - +
80B PHE 3.7 1.2 + - - -
76E GLY* 5.8 0.6 - - - -
77E ARG* 5.3 5.9 + - - +
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Residues in contact with ARG 79 (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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14B THR* 5.6 4.9 - - + +
15B PRO* 5.1 16.7 - - + +
16B ASP* 4.5 16.7 + - - -
70B LYS* 3.4 2.9 - - - -
71B ASP* 2.7 45.7 + - + +
73B GLU* 4.3 23.3 + - + +
77B ARG* 4.0 34.2 - - + +
78B ASN* 1.3 72.6 - - - +
80B PHE* 1.3 75.8 + - - +
81B LEU* 3.8 8.9 - - + +
77E ARG* 4.6 24.5 - - + +
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Residues in contact with PHE 80 (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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15B PRO* 5.6 0.9 - - - +
68B VAL* 3.6 28.7 - - + -
70B LYS* 3.9 13.8 - - + +
78B ASN 3.7 4.2 + - - -
79B ARG* 1.3 85.4 - - - +
81B LEU* 1.3 66.3 + - - +
82B GLY* 3.6 21.1 - - - -
83B GLU* 3.4 45.8 - - + -
106B LEU 3.7 2.0 - - - -
107B ASP* 3.6 3.6 - - + -
108B THR* 3.4 35.4 - - + -
77E ARG* 3.6 41.8 - - + +
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Residues in contact with LEU 81 (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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12B VAL* 3.6 31.2 - - + -
13B HIS 4.1 7.4 - - - +
14B THR* 3.9 28.7 - - + +
15B PRO* 4.1 10.1 - - + -
20B SER* 4.6 3.8 - - - +
22B ALA* 4.6 1.1 - - + -
69B VAL* 2.9 18.4 + - + +
70B LYS 3.8 6.1 - - - +
71B ASP* 3.6 42.8 - - + +
79B ARG* 4.2 2.5 - - + +
80B PHE* 1.3 90.9 - - - +
82B GLY* 1.3 60.4 + - - +
107B ASP* 4.3 3.5 - - - +
113B THR* 3.8 16.2 - - - +
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Residues in contact with GLY 82 (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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68B VAL* 3.5 3.3 - - - +
69B VAL* 2.8 29.6 + - - +
80B PHE* 3.6 6.0 - - - -
81B LEU* 1.3 81.5 - - - +
83B GLU* 1.3 62.5 + - - +
105B LEU* 4.2 21.5 - - - -
106B LEU 3.4 11.7 - - - -
113B THR* 4.6 2.2 - - - -
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Residues in contact with GLU 83 (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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66B HIS* 2.9 29.1 + - - +
67B VAL 3.2 12.8 - - - +
68B VAL* 4.2 3.5 - - + +
80B PHE* 3.4 30.5 - - + -
82B GLY* 1.3 74.3 - - - +
84B ALA* 1.3 65.7 + - - +
85B LYS* 5.7 3.1 - - - -
105B LEU* 3.5 5.9 - - - +
106B LEU* 2.8 44.6 + - + +
107B ASP 3.9 7.3 - - - +
108B THR* 4.5 4.3 - - - +
110B LYS* 3.8 23.5 + - - +
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Residues in contact with ALA 84 (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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208A FMT 3.7 14.4 - - - +
66B HIS* 3.4 4.2 - - - -
67B VAL* 2.9 44.4 + - + +
83B GLU* 1.3 78.7 - - - +
85B LYS* 1.3 64.5 + - - +
103B ALA* 4.1 14.1 - - + -
104B PRO 3.8 17.9 - - - +
105B LEU* 3.9 11.2 - - + -
106B LEU* 5.9 0.2 - - - -
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Residues in contact with LYS 85 (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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61A GLN* 3.7 27.3 + - + +
208A FMT 3.3 14.6 + - - +
64B GLU* 3.8 32.1 + - + +
65B LEU 3.4 6.5 - - - +
66B HIS* 3.7 31.9 + - + +
83B GLU* 5.7 2.9 - - - -
84B ALA* 1.3 77.2 - - - +
86B VAL* 1.3 63.5 + - - +
87B PRO* 3.8 4.2 - - - +
110B LYS* 5.2 14.4 - - - +
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Residues in contact with VAL 86 (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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64B GLU* 3.4 4.6 - - - -
65B LEU* 3.0 60.4 + - + +
67B VAL* 5.1 7.6 - - + -
85B LYS* 1.3 79.8 - - - +
87B PRO* 1.3 68.0 - - + +
88B LEU* 3.3 10.0 + - + +
101B PHE* 4.1 35.7 - - + -
103B ALA* 4.3 18.2 - - + -
119B LEU* 4.4 16.2 - - + -
121B VAL* 5.1 0.2 - - + -
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Residues in contact with PRO 87 (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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61A GLN* 5.5 5.8 - - - +
62B GLY* 6.2 1.6 - - - -
63B SER 4.2 0.7 - - - +
64B GLU* 4.1 18.6 - - + +
85B LYS 3.8 7.0 - - - +
86B VAL* 1.3 82.6 - - + +
88B LEU* 1.3 58.9 + - - +
89B ARG* 3.0 43.4 + - + +
90B GLU* 3.2 37.3 + - - +
101B PHE* 3.6 13.0 - - + -
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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