Contacts of the strand formed by residues 4 - 10 (chain A) in PDB entry 6ABP
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 LYS 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ASN 3.6 16.0 + - - +
3A LEU* 1.3 80.8 - - - +
5A LEU* 1.3 68.0 - - - +
34A GLU* 3.4 33.0 - - - +
36A ILE* 3.7 30.5 - - + -
56A SER* 3.0 26.1 + - - +
57A GLY* 4.1 10.9 + - - -
58A ALA* 3.2 9.9 - - - +
59A LYS* 3.2 26.5 + - - +
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Residues in contact with LEU 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 LEU* 4.3 6.5 - - + -
4A LYS* 1.3 84.9 - - - +
6A GLY* 1.3 63.5 + - - +
33A PHE* 3.7 36.3 - - + -
34A GLU 2.7 9.8 + - - +
35A VAL* 3.2 8.8 - - + +
36A ILE* 2.8 24.3 + - - -
58A ALA* 4.5 2.2 - - - -
59A LYS* 4.2 10.5 - - + -
60A GLY* 3.5 22.7 - - - +
264A SER* 4.5 1.3 - - - +
267A LEU* 4.1 22.9 - - + -
268A TYR* 4.0 31.6 - - + +
271A VAL* 4.3 11.0 - - + -
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Residues in contact with GLY 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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5A LEU* 1.3 75.5 - - - +
7A PHE* 1.3 61.8 + - - +
8A LEU* 4.2 0.4 - - - -
35A VAL* 4.7 0.4 - - - -
36A ILE 3.4 8.7 - - - -
53A LEU* 4.0 19.4 - - - +
58A ALA* 4.5 0.2 - - - +
60A GLY 2.8 13.5 + - - -
61A PHE* 3.1 15.7 - - - -
62A VAL* 2.9 25.1 + - - +
267A LEU* 4.5 1.4 - - - +
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Residues in contact with PHE 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 LEU 4.1 0.2 + - - -
6A GLY* 1.3 72.5 - - - -
8A LEU* 1.4 62.8 + - - +
9A VAL* 3.6 15.3 - - + -
20A GLU* 3.7 38.8 - - + -
21A TRP* 2.9 41.3 + + + -
24A ALA* 3.5 11.2 - - + -
35A VAL* 3.7 19.1 - - + -
36A ILE 2.9 8.5 + - - +
37A LYS* 3.6 0.7 - - - -
38A ILE 3.2 14.2 + - - -
62A VAL* 3.5 29.2 - - + -
88A VAL* 4.3 6.3 - - + -
259A HIS 4.7 0.2 - - - -
260A GLY* 3.8 10.5 - - - -
263A SER* 3.6 21.1 - - - -
264A SER* 3.5 22.2 - - - -
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Residues in contact with LEU 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 GLY* 4.1 2.0 - - - -
7A PHE* 1.4 88.0 - - - +
9A VAL* 1.3 65.5 + - - +
38A ILE* 3.3 24.0 - - + +
40A VAL* 3.8 28.5 - - + -
46A THR 4.8 0.4 - - - +
49A ALA* 4.2 12.6 - - + -
50A ILE* 4.4 13.5 - - + -
53A LEU* 3.8 22.7 - - + -
61A PHE* 4.3 13.2 - - + -
62A VAL 2.8 13.0 + - - +
63A ILE* 3.3 24.2 - - + +
64A CYS 2.8 26.7 + - - -
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Residues in contact with VAL 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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7A PHE* 3.6 29.2 - - + -
8A LEU* 1.3 80.5 - - - +
10A LYS* 1.3 63.0 + - - +
12A PRO* 4.0 13.1 - - + +
17A PHE* 3.7 42.4 - - + +
20A GLU* 4.4 0.2 - - - +
21A TRP* 3.6 35.4 - - + +
38A ILE 3.0 5.5 + - - -
39A ALA* 3.5 2.6 - - - -
40A VAL* 2.8 23.0 + - - +
64A CYS* 3.6 5.6 - - + -
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Residues in contact with LYS 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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9A VAL* 1.3 74.2 - - - +
11A GLN* 1.4 86.8 + - + +
12A PRO* 3.6 5.3 - - - +
17A PHE* 3.8 17.9 - - + -
40A VAL 3.4 11.2 - - - -
41A PRO* 3.4 22.3 - - - +
64A CYS* 2.9 21.6 + - - +
65A THR 3.5 15.7 - - - +
66A PRO* 3.6 25.8 - - + +
90A ASP* 2.7 22.6 + - - +
145A LEU* 4.0 10.9 - - - +
177A ASN* 4.8 4.8 - - - +
307A ARA 2.8 34.1 + - - -
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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