Contacts of the strand formed by residues 112 - 124 (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 PRO 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A PHE 5.7 4.0 - - - +
97A LEU* 3.6 31.4 - - + -
123A TYR* 3.5 39.9 - - + +
105B LEU 3.7 7.9 - - - +
106B LEU* 3.8 11.4 - - + -
107B ASP* 5.1 1.0 - - - +
110B LYS 4.1 1.8 - - - +
111B GLN* 1.3 89.8 - - + +
113B THR* 1.3 60.5 + - - +
114B GLY 3.5 1.3 - - - +
205B FMT 3.9 5.2 - - - +
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Residues in contact with THR 113 (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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11B ASN 5.1 1.6 - - - +
13B HIS* 6.0 0.3 + - - -
81B LEU 3.8 16.4 - - - +
82B GLY* 4.6 1.2 - - - -
105B LEU* 2.9 20.3 + - - +
106B LEU 3.9 1.6 - - - -
107B ASP* 3.5 39.3 - - + +
112B PRO* 1.3 73.7 - - - +
114B GLY* 1.3 57.2 + - - +
115B ALA* 3.2 26.0 + - - +
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 6.2 0.2 - - - -
11B ASN* 3.2 26.1 - - - +
112B PRO* 3.5 2.8 - - - +
113B THR* 1.3 78.4 - - - +
115B ALA* 1.3 59.1 + - - +
205B FMT 3.2 20.8 + - - -
206B FMT 3.5 9.0 + - - -
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Residues in contact with ALA 115 (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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10B GLU 3.1 10.3 - - - +
11B ASN 3.2 20.8 + - - +
12B VAL* 4.3 9.2 - - + -
13B HIS 5.4 0.2 - - - +
105B LEU* 2.7 47.3 + - + +
113B THR* 3.2 16.2 + - - +
114B GLY* 1.3 80.3 - - - +
116B SER* 1.3 54.9 + - - +
205B FMT 3.1 6.3 + - - -
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Residues in contact with SER 116 (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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95A PRO* 3.7 15.9 - - - +
9B ALA* 3.1 6.6 - - - +
10B GLU* 2.9 43.9 + - - +
102B ASN* 3.6 18.2 + - - -
103B ALA 3.2 12.6 - - - -
104B PRO* 4.4 0.9 - - - -
105B LEU* 4.2 4.2 - - - +
114B GLY 4.0 0.4 + - - -
115B ALA* 1.3 75.0 - - - +
117B LEU* 1.3 61.4 + - - +
118B VAL* 5.5 1.2 - - - +
205B FMT 4.7 0.2 - - - -
206B FMT 2.9 22.5 + - - -
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Residues in contact with LEU 117 (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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6B ILE* 3.9 16.2 - - + -
8B TYR 3.4 16.8 - - - +
9B ALA* 4.0 3.6 - - + -
24B CYS* 4.1 12.6 - - - -
46B TRP* 3.7 24.0 - - + -
67B VAL* 3.6 38.4 - - + -
69B VAL* 4.5 3.8 - - + -
101B PHE 3.4 2.9 - - - +
103B ALA* 2.8 41.1 + - + +
105B LEU* 4.0 20.0 - - + -
116B SER* 1.3 75.6 - - - +
118B VAL* 1.3 65.3 + - - +
119B LEU* 3.9 19.5 - - + +
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Residues in contact with VAL 118 (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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6B ILE* 3.9 0.7 - - - -
7B LEU* 2.9 39.5 + - + +
8B TYR* 2.8 64.5 + - + +
10B GLU* 5.7 0.9 - - + -
100B SER* 6.1 2.5 - - - -
101B PHE 3.3 8.3 - - - +
102B ASN* 3.5 31.4 - - + +
116B SER* 5.5 2.0 - - - +
117B LEU* 1.3 75.2 - - - +
119B LEU* 1.3 67.4 + - - +
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Residues in contact with LEU 119 (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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4B VAL* 4.0 6.7 - - + -
5B PHE 3.2 14.8 - - - +
6B ILE* 4.2 9.0 - - + -
7B LEU* 4.3 3.1 - - - +
65B LEU* 3.6 31.0 - - + -
67B VAL* 4.7 7.0 - - + -
86B VAL* 4.4 16.6 - - + -
100B SER* 3.4 4.7 - - - -
101B PHE* 2.8 56.4 + - + +
103B ALA* 5.1 2.5 - - + -
117B LEU* 3.9 26.5 - - + +
118B VAL* 1.3 83.2 - - - +
120B GLN* 1.3 60.4 + - - +
121B VAL* 3.8 16.4 - - + -
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Residues in contact with GLN 120 (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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3B ARG 4.7 0.3 - - - +
4B VAL* 3.4 3.6 - - - +
5B PHE* 2.9 61.5 + - + +
7B LEU* 5.0 9.1 - - + +
98B SER* 3.8 27.1 + - - -
99B ALA 3.6 10.8 + - - +
100B SER* 4.2 11.4 - - - +
119B LEU* 1.3 74.7 - - - +
121B VAL* 1.3 72.0 + - - +
122B SER* 4.3 7.3 + - - -
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Residues in contact with VAL 121 (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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2B LEU* 3.5 28.0 - - + -
3B ARG 3.4 6.3 - - - +
4B VAL* 4.1 13.2 - - + -
65B LEU* 4.5 4.7 - - + -
88B LEU* 4.1 9.6 - - + -
91B VAL* 3.9 17.3 - - + +
98B SER* 3.2 4.2 - - - -
99B ALA 2.8 36.0 + - - +
101B PHE* 4.1 19.3 - - + -
119B LEU* 3.8 24.9 - - + -
120B GLN* 1.3 82.7 + - - +
122B SER* 1.3 64.7 + - - +
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Residues in contact with SER 122 (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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1B MET 3.6 0.3 - - - +
2B LEU* 3.6 4.5 - - - +
3B ARG* 2.8 75.2 + - - +
91B VAL* 4.1 2.9 - - - -
96B SER 5.4 0.4 - - - -
97B LEU 3.3 13.2 - - - -
98B SER* 3.6 11.2 - - - -
120B GLN* 4.3 8.3 + - - -
121B VAL* 1.3 78.7 - - - +
123B TYR* 1.3 67.5 + - - +
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Residues in contact with TYR 123 (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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0B PHE* 5.7 6.1 - - + -
1B MET 3.5 3.4 - - - +
2B LEU* 3.4 27.8 - - + +
28B PHE* 5.7 0.4 - + - -
54B LEU* 3.4 24.2 - - + -
59B LEU* 3.2 43.9 - - + +
63B SER* 5.2 0.2 + - - -
88B LEU* 3.8 24.3 + - - +
91B VAL* 3.5 30.1 - - + -
92B LEU* 3.4 33.7 - - + +
96B SER 5.0 1.6 - - - +
97B LEU* 3.0 37.6 + - + +
122B SER* 1.3 74.1 - - - +
124B THR* 1.3 60.3 + - - +
112C PRO* 4.5 7.0 - - + -
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Residues in contact with THR 124 (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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0B PHE* 3.6 7.3 - - - +
1B MET* 3.1 45.5 + - + +
3B ARG* 3.5 52.3 + - + +
51B GLU* 4.4 9.2 - - - +
122B SER* 4.7 0.4 - - - -
123B TYR* 1.3 75.4 - - - +
125B ALA* 1.3 70.7 + - - +
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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