Contacts of the strand formed by residues 90 - 95 (chain A) in PDB entry 1A4J
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 3.3 1.5 - - - +
43A GLN* 2.7 49.4 + - + +
45A PRO* 6.2 1.6 - - + -
89A GLY* 1.3 76.2 - - - -
91A TYR* 1.3 64.6 + - - +
92A PHE* 3.5 33.1 - - + -
106A GLY* 3.8 4.5 - - - -
107A THR 3.2 21.8 - - - +
108A LYS* 3.8 24.0 - - + +
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Residues in contact with TYR 91 (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 GLN* 2.7 27.5 + - - +
21A ILE* 3.8 25.6 - - + -
40A TRP* 4.9 4.7 - - + -
41A TYR 3.2 13.5 - - - +
42A LEU* 3.4 19.2 - - + +
52A LEU* 3.5 26.0 - - + -
67A PHE* 3.6 12.2 - + - -
78A LEU* 3.5 24.9 - - + -
80A ILE* 3.5 18.5 - - + +
87A ASP* 2.5 38.3 + - - +
89A GLY 4.1 3.1 - - - -
90A VAL* 1.3 72.8 - - - +
92A PHE* 1.3 56.0 + - - +
106A GLY* 3.0 1.6 - - - -
107A THR* 2.8 30.1 + - - +
109A LEU* 3.9 18.8 - - + -
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Residues in contact with PHE 92 (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 GLN* 3.5 1.6 - - - -
40A TRP* 3.4 5.8 - - - -
41A TYR* 2.7 53.8 + - + +
43A GLN* 3.2 39.0 - - + -
49A PRO* 5.3 0.9 - - + -
90A VAL* 3.5 30.1 - - + -
91A TYR* 1.3 74.0 - - - +
93A CYS* 1.3 63.9 + - - +
103A PHE* 4.6 7.2 - - + -
104A GLY 3.4 19.1 - - - -
105A GLY 3.6 9.4 - - - -
106A GLY* 3.5 17.9 - - - -
39B GLN* 4.4 6.3 - - - -
43B LYS 5.5 0.7 - - - -
44B GLY* 4.9 10.8 - - - -
45B LEU* 3.9 30.7 - - + -
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Residues in contact with CYS 93 (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 MET* 4.1 4.0 - - - -
6A GLN* 3.2 26.3 + - - -
23A CYS* 2.0 54.1 - - + -
38A LEU* 4.5 2.9 - - + -
39A HIS 3.2 8.3 - - - +
40A TRP* 3.7 18.1 - - + -
92A PHE* 1.3 74.9 - - - +
94A SER* 1.3 65.5 + - - +
103A PHE* 3.4 3.8 - - - +
104A GLY* 2.8 31.0 + - - -
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Residues in contact with SER 94 (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 MET* 4.5 2.0 - - - -
37A TYR 3.7 0.5 - - - +
38A LEU* 3.3 8.9 - - - +
39A HIS* 2.7 42.2 + - - -
41A TYR* 3.5 30.2 + - - -
93A CYS* 1.3 78.7 - - - +
95A GLN* 1.3 67.2 + - - +
96A SER* 5.6 0.5 - - - -
102A THR 3.3 10.2 + - - -
103A PHE* 3.7 20.2 - - - +
106B PHE* 4.3 10.2 - - - -
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Residues in contact with GLN 95 (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* 3.1 30.7 - - + +
4A MET* 3.3 19.4 - - - -
29A LEU* 3.8 19.3 - - + -
37A TYR 3.3 4.5 - - - +
94A SER* 1.3 75.9 + - - +
96A SER* 1.3 62.8 + - - +
97A THR* 3.5 9.0 + - - +
98A HIS* 2.9 38.1 + - - +
100A PRO 3.6 4.5 + - - +
101A PRO* 3.3 6.4 - - - +
102A THR* 2.5 59.1 + - - +
106B PHE* 5.8 0.2 - - - -
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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