Contacts of the strand formed by residues 1 - 10 (chain A) 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 MET 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A PHE* 1.3 80.6 - - + +
2A LEU* 1.3 61.8 + - - +
3A ARG* 3.9 1.3 + - + +
51A GLU* 2.3 70.4 - - + +
52A TRP 3.3 13.0 - - - +
53A ASP* 4.5 6.1 - - + +
54A LEU* 4.4 6.5 - - - -
122A SER 3.7 0.3 - - - +
123A TYR* 3.6 5.0 - - - -
124A THR* 2.8 49.7 + - + +
125A ALA 4.7 11.7 - - - +
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Residues in contact with LEU 2 (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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1A MET* 1.3 73.6 - - - +
3A ARG* 1.3 59.3 + - - +
4A VAL* 4.1 17.9 - - + -
28A PHE* 3.8 27.8 - - + -
50A PHE 3.9 0.5 - - - +
51A GLU* 3.5 2.3 - - - -
52A TRP* 2.9 49.5 + - + -
54A LEU* 4.1 12.2 - - + +
59A LEU* 4.2 25.1 - - + -
65A LEU* 4.7 2.7 - - + -
88A LEU* 3.9 17.7 - - + -
91A VAL* 5.6 0.9 - - + -
121A VAL* 3.5 26.0 - - + -
122A SER 3.5 9.4 - - - +
123A TYR* 4.7 2.5 - - + +
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Residues in contact with ARG 3 (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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1A MET* 3.9 1.3 + - + -
2A LEU* 1.3 72.8 - - - +
4A VAL* 1.3 63.3 + - - +
5A PHE* 3.5 39.1 - - + -
50A PHE 3.3 11.2 - - - +
51A GLU* 4.1 24.8 + - + +
120A GLN 3.9 0.2 - - - +
121A VAL* 3.4 3.5 - - - +
122A SER* 2.7 70.9 + - - +
124A THR* 3.8 30.2 + - + +
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Residues in contact with VAL 4 (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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2A LEU* 4.1 8.7 - - + -
3A ARG* 1.3 77.7 - - - +
5A PHE* 1.3 67.5 + - - +
6A ILE* 3.9 23.5 + - + -
48A GLU 3.6 1.2 - - - +
49A GLY* 3.5 1.4 - - - -
50A PHE* 2.8 42.0 + - + +
52A TRP* 3.5 30.5 - - + -
65A LEU* 3.8 29.8 - - + -
119A LEU* 4.4 7.2 - - + -
120A GLN 3.3 7.4 - - - +
121A VAL* 3.9 15.0 - - + -
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Residues in contact with PHE 5 (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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3A ARG* 3.5 42.2 - - + -
4A VAL* 1.3 73.0 - - - +
6A ILE* 1.3 62.4 - - - +
7A LEU* 3.5 20.5 + - + +
47A ASN* 5.8 2.9 - - - -
48A GLU 3.3 4.5 - - - +
49A GLY* 3.8 23.3 - - - -
119A LEU* 3.1 5.9 - - - -
120A GLN* 2.7 63.0 + - + +
122A SER* 5.5 2.0 - - - -
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Residues in contact with ILE 6 (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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4A VAL* 4.0 11.4 - - + -
5A PHE* 1.3 69.9 - - - +
7A LEU* 1.3 60.6 + - - +
24A CYS* 3.4 29.2 - - + +
26A ALA* 4.3 16.4 - - + -
35A THR* 4.2 10.3 - - + -
46A TRP* 3.8 25.2 - - + +
47A ASN 3.1 6.1 + - - -
48A GLU 2.9 32.8 + - - +
50A PHE* 3.8 26.9 - - + -
67A VAL* 4.5 9.0 - - + -
117A LEU* 4.0 19.1 - - + -
118A VAL 4.2 2.2 - - - +
119A LEU* 4.3 4.5 - - + -
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Residues in contact with LEU 7 (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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5A PHE* 3.8 30.1 - - + +
6A ILE* 1.3 73.4 - - - +
8A TYR* 1.3 82.7 + - + +
45A VAL* 3.6 5.6 - - - +
46A TRP* 3.0 9.1 + - - -
47A ASN* 3.0 42.3 + - - +
118A VAL* 3.0 29.5 + - + +
119A LEU* 4.7 1.3 - - - -
120A GLN* 5.0 8.7 - - + +
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Residues in contact with TYR 8 (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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6A ILE* 3.9 0.4 - - - +
7A LEU* 1.3 96.9 - - + +
9A ALA* 1.3 59.8 + - - +
10A GLU* 3.6 28.9 - - + -
43A ASN* 5.2 1.8 - - + +
44A PRO 3.1 17.0 - - - +
45A VAL* 3.8 18.4 - - + -
46A TRP* 3.7 10.2 - - - -
102A ASN* 5.1 0.2 + - - -
117A LEU* 3.3 3.8 - - - +
118A VAL* 2.8 60.7 + - + +
205A FMT 2.6 29.8 + - - -
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Residues in contact with ALA 9 (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 TYR* 1.3 77.3 - - - +
10A GLU* 1.3 67.1 + - - +
12A VAL* 3.6 17.7 - - + -
43A ASN* 3.3 24.8 - - - +
44A PRO* 3.1 9.5 + - + +
46A TRP* 3.5 25.0 - - + -
69A VAL* 5.1 0.9 - - + -
105A LEU* 4.9 6.7 - - + -
116A SER 3.1 14.4 - - - +
117A LEU* 4.1 7.0 - - + -
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Residues in contact with GLU 10 (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 TYR* 3.6 23.0 - - + -
9A ALA* 1.3 75.7 - - - +
11A ASN* 1.3 79.7 + - - +
12A VAL* 3.3 3.6 + - - +
42A VAL 4.1 0.2 - - - -
43A ASN* 3.7 16.9 - - + +
115A ALA* 3.3 2.3 - - - +
116A SER* 3.0 37.2 + - - +
205A FMT 3.0 39.3 + - - +
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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