Contacts of the strand formed by residues 18 - 25 (chain A) in PDB entry 6U6V
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR* 3.6 30.7 - - + -
12A CYS* 3.9 2.0 - - - -
17A ASN* 1.3 75.2 - - - +
19A THR* 1.3 67.1 + - - +
20A LEU* 4.1 10.3 - - + -
99A ILE 3.8 0.9 - - - +
100A THR* 3.4 3.1 - - - +
101A MET* 2.8 41.7 + - + +
104A LEU* 3.6 29.8 - - + +
134A LEU* 4.2 13.9 - - + -
146A CYS* 3.8 22.9 - - + -
148A VAL* 5.7 0.2 - - + -
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Residues in contact with THR 19 (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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10A TYR* 3.5 17.2 + - - -
18A VAL* 1.3 76.6 - - - +
20A LEU* 1.3 61.2 + - - +
21A THR* 4.1 10.2 + - - +
98A SER* 3.7 27.1 - - - +
99A ILE 3.3 4.0 - - - +
100A THR* 3.0 30.7 + - - +
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Residues in contact with LEU 20 (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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10A TYR* 3.7 44.6 - - + -
18A VAL* 4.1 17.0 - - + -
19A THR* 1.3 73.3 - - - +
21A THR* 1.3 58.8 + - - +
40A TRP* 3.7 5.8 - - + -
98A SER* 3.1 6.6 - - - -
99A ILE* 2.9 49.5 + - + +
101A MET* 4.2 8.3 - - - -
112A TYR* 3.6 49.1 - - + -
132A MET* 3.8 13.9 - - + -
134A LEU* 4.6 7.9 - - + -
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Residues in contact with THR 21 (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 THR* 4.1 0.2 - - - -
6A PRO* 3.4 37.4 - - + +
7A TYR* 5.3 3.6 - - - +
10A TYR* 3.4 10.1 + - - -
19A THR* 4.1 15.8 + - - +
20A LEU* 1.3 77.2 + - - +
22A CYS* 1.3 78.6 + - - +
23A ARG* 4.0 10.3 - - + -
40A TRP* 4.0 1.5 - - - -
96A ASN* 4.7 8.7 - - + +
97A PHE 3.5 7.6 - - - +
98A SER* 4.2 3.9 - - - -
132A MET* 3.6 11.4 - - - +
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Residues in contact with CYS 22 (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 VAL* 3.7 12.6 - - + -
4A ALA 3.4 6.3 - - - -
5A THR* 4.1 5.2 - - - -
21A THR* 1.3 73.7 - - - +
23A ARG* 1.3 65.6 + - - +
24A LEU* 5.7 2.0 - - + -
40A TRP* 3.8 1.6 - - + -
95A GLY 4.5 0.2 - - - -
96A ASN 3.8 0.3 - - - -
97A PHE* 2.8 41.3 + - + +
114A CYS* 2.0 52.9 - - + -
116A VAL* 5.8 0.2 - - + -
132A MET* 3.4 26.0 - - - -
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Residues in contact with ARG 23 (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 VAL* 3.4 3.6 - - - -
4A ALA* 2.7 51.4 + - + +
6A PRO* 4.0 20.2 - - + -
21A THR* 4.0 11.0 - - + -
22A CYS* 1.3 78.2 - - - +
24A LEU* 1.3 61.9 + - - +
25A LEU* 3.3 24.6 - - + +
94A HIS 5.6 4.0 + - - -
95A GLY 3.2 6.5 - - - +
96A ASN* 3.6 22.7 + - - +
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Residues in contact with LEU 24 (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 PHE* 3.3 36.8 - - + -
2A LYS 3.9 6.7 - - - +
3A VAL* 3.5 30.1 - - + -
22A CYS* 5.7 1.6 - - + -
23A ARG* 1.3 75.1 - - - +
25A LEU* 1.3 72.9 + - - +
26A GLY 4.3 2.8 + - - +
36A PHE* 5.1 4.0 - - + -
38A LYS* 4.7 11.0 - - - +
94A HIS 4.9 2.1 - - - +
95A GLY* 2.6 35.8 + - - +
97A PHE* 5.7 3.8 - - + -
116A VAL* 3.7 26.0 - - + -
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Residues in contact with LEU 25 (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 PHE* 4.1 4.2 - - - -
2A LYS* 3.2 39.9 + - + +
3A VAL 4.1 0.7 - - - -
4A ALA* 3.6 21.1 - - + +
23A ARG* 3.3 43.3 - - - +
24A LEU* 1.3 88.7 - - - +
26A GLY* 1.3 58.3 + - - +
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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