Contacts of the strand formed by residues 45 - 53 (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 VAL 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B LEU 3.6 11.0 - - - +
8B TYR* 3.8 17.5 - - + -
36B LYS* 4.9 0.7 + - - -
38B ILE* 3.5 20.8 - - - +
43B ASN* 3.4 18.7 + - - +
44B PRO* 1.3 74.9 - - - +
46B TRP* 1.3 62.6 + - - +
47B ASN* 4.2 15.5 - - + -
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Residues in contact with TRP 46 (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* 3.8 24.0 - - + +
7B LEU 2.9 4.8 + - - -
8B TYR* 3.7 11.4 - - - -
9B ALA* 3.5 31.6 - - + -
22B ALA* 3.2 28.9 + - + -
23B TYR* 3.6 7.6 - - - +
24B CYS* 4.1 6.7 - - + -
35B THR* 3.0 36.3 + - + -
36B LYS* 3.0 45.3 + - - +
38B ILE* 3.6 13.8 - - + +
44B PRO* 3.5 29.6 - - + -
45B VAL* 1.3 73.8 - - - +
47B ASN* 1.3 75.1 + - - +
48B GLU* 3.2 7.9 + - - +
69B VAL* 4.4 10.3 - - + -
117B LEU* 3.7 11.9 - - + -
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Residues in contact with ASN 47 (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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5B PHE* 5.6 5.5 - - - -
6B ILE 3.1 6.7 + - - -
7B LEU* 2.9 35.2 + - + +
45B VAL* 4.2 15.5 - - + -
46B TRP* 1.3 78.3 - - - +
48B GLU* 1.3 59.4 + - - +
49B GLY 4.2 0.9 + - - -
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Residues in contact with GLU 48 (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 3.6 0.5 - - - +
5B PHE* 3.2 5.5 - - - -
6B ILE 2.9 30.6 + - - -
34B ARG 4.3 1.0 - - - +
35B THR* 3.4 22.8 - - + -
36B LYS* 2.8 52.6 + - - +
46B TRP* 3.4 15.1 - - + +
47B ASN* 1.3 76.2 - - - +
49B GLY* 1.3 62.6 + - - +
50B PHE* 3.8 24.7 - - + -
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Residues in contact with GLY 49 (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* 5.9 0.7 - - - -
4B VAL 3.4 5.4 - - - -
5B PHE* 3.6 23.1 - - - -
47B ASN 4.2 1.2 + - - -
48B GLU* 1.3 74.5 - - - +
50B PHE* 1.3 72.2 + - - -
51B GLU* 5.7 0.7 - - - -
203B FMT 3.7 6.4 + - - -
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Residues in contact with PHE 50 (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 4.3 0.7 - - - -
3B ARG* 3.3 1.4 - - - +
4B VAL* 2.7 40.6 + - + +
6B ILE* 3.9 17.9 - - + -
26B ALA* 5.7 0.7 - - + -
33B LYS* 3.7 31.9 - - + -
34B ARG* 3.5 35.2 - - - -
35B THR* 3.8 21.1 - - + -
48B GLU* 3.8 31.0 - - + -
49B GLY* 1.3 78.3 - - - -
51B GLU* 1.3 70.8 + - - +
52B TRP* 3.8 15.7 - + + -
203B FMT 3.6 15.0 - - - -
204B FMT 3.8 13.5 - - - -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 3.4 35.9 - - + +
2B LEU 3.2 4.7 - - - +
3B ARG* 3.8 33.2 + - + +
33B LYS* 3.3 15.7 + - - -
49B GLY 5.7 0.2 - - - -
50B PHE* 1.3 83.3 - - - +
52B TRP* 1.3 61.0 + - - +
53B ASP 4.2 0.2 + - - -
124B THR* 4.4 4.9 - - - +
201B FMT 3.5 4.5 + - - -
203B FMT 2.9 25.4 + - - +
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Residues in contact with TRP 52 (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* 3.1 7.0 - - - -
2B LEU* 2.8 51.2 + - + +
4B VAL* 3.6 27.8 - - + -
26B ALA* 3.6 39.3 - - + -
28B PHE* 3.1 50.6 + + + -
29B ALA* 4.9 2.2 - - + -
31B VAL* 2.9 33.9 + - + +
33B LYS* 3.4 32.4 - - + +
50B PHE* 3.8 19.1 - + + -
51B GLU* 1.3 76.3 - - - +
53B ASP* 1.3 65.2 + - - +
54B LEU* 4.1 0.3 - - - +
65B LEU* 4.1 7.0 - - + -
201B FMT 3.6 6.3 - - - +
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Residues in contact with ASP 53 (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 3.5 6.2 + - - +
1B MET* 3.6 15.3 - - + +
29B ALA* 5.5 0.5 - - - +
51B GLU 4.2 0.6 + - - -
52B TRP* 1.3 73.6 - - - +
54B LEU* 1.3 71.0 + - - +
55B LYS* 3.2 32.2 + - - +
57B ILE* 3.3 17.3 - - - +
201B FMT 2.9 18.2 + - - +
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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