Contacts of the strand formed by residues 3 - 9 (chain A) in PDB entry 3C7N
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 THR 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 73.0 - - - +
4A PRO* 1.3 81.1 - - - +
5A PHE* 3.5 2.6 + - - +
18A VAL* 3.6 21.5 - - + -
19A ALA 3.3 21.7 + - - +
20A ARG* 4.5 7.3 - - + +
134A THR* 4.6 9.2 - - + +
136A ALA* 4.4 13.7 - - - +
137A ASN 3.0 9.2 + - - +
138A ILE* 4.0 27.7 - - + +
139A THR 4.7 2.1 + - - -
140A ASP* 4.3 8.4 + - - +
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Residues in contact with PRO 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 SER 3.8 6.3 - - - +
3A THR* 1.3 85.8 - - - +
5A PHE* 1.3 59.4 + - - +
6A GLY 4.2 0.4 + - - -
18A VAL* 3.3 5.9 - - - -
19A ALA* 3.0 54.1 + - + +
140A ASP* 4.7 2.2 - - + +
377A ALA* 4.0 1.3 - - - +
380A CYS* 3.9 12.3 - - + -
381A ALA* 3.7 26.2 - - - +
384A SER* 4.1 7.0 - - - -
387A LEU* 3.3 31.6 - - + -
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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 THR 3.5 2.8 + - - +
4A PRO* 1.3 75.4 - - - +
6A GLY* 1.3 78.9 + - - +
7A LEU* 3.8 20.0 - - + -
16A LEU* 4.1 10.1 - - + -
17A ALA 3.5 9.2 - - - +
18A VAL* 4.7 5.8 - - + -
126A VAL* 4.1 18.8 - - + -
127A LYS* 4.2 13.2 - - - -
130A VAL* 4.0 27.1 - - + -
138A ILE* 3.9 24.0 - - + -
140A ASP 3.7 7.2 + - - +
141A VAL* 3.2 35.0 - - + +
142A CYS 3.1 20.8 + - - -
166A LEU* 4.1 11.4 - - + -
380A CYS* 3.5 8.1 - - - -
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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 PHE* 1.3 77.6 - - - +
7A LEU* 1.3 60.0 + - - -
15A VAL 4.0 0.9 - - - +
17A ALA* 3.1 34.9 + - - +
142A CYS 3.3 10.1 - - - -
373A ALA 4.4 2.4 - - - +
376A ALA* 4.0 6.5 - - - -
377A ALA* 3.4 29.3 - - - +
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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 16.5 + - + -
6A GLY* 1.3 73.9 - - - -
8A ASP* 1.3 68.9 + - - +
9A LEU* 3.7 29.4 - - + +
14A SER* 3.6 31.0 - - - +
15A VAL 4.0 1.6 - - - -
16A LEU* 4.0 14.1 - - + -
122A PHE* 5.0 1.3 - - + -
123A ILE* 4.1 19.3 - - + -
126A VAL* 4.5 14.6 - - + -
141A VAL* 4.7 3.6 - - + -
142A CYS 3.0 9.1 + - - +
143A ILE* 3.5 18.1 - - + -
144A ALA* 3.0 26.0 + - - +
373A ALA* 5.0 0.4 - - - -
376A ALA* 4.5 4.5 - - - +
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Residues in contact with ASP 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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7A LEU* 1.3 73.3 - - - +
9A LEU* 1.3 59.7 + - - +
10A GLY 3.0 9.2 + - - -
13A ASN 5.4 1.5 - - - +
14A SER* 3.1 19.9 - - - -
15A VAL* 3.2 17.2 + - - +
144A ALA* 4.4 8.8 - - - +
174A ASP* 5.0 0.9 - - - +
369A ASP 4.5 8.5 - - - +
372A ILE* 3.6 33.8 - - + +
373A ALA* 3.5 28.5 + - + +
671A BEF 3.1 28.3 - - - -
672A ADP 5.1 0.2 + - - -
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Residues in contact with LEU 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 LEU* 3.7 28.7 + - + -
8A ASP* 1.3 71.1 + - - +
10A GLY* 1.3 59.0 + - - +
14A SER* 3.8 13.9 - - - +
38A SER* 5.2 4.3 - - - +
68A LEU* 4.9 9.9 - - + -
69A LYS* 2.7 57.3 - - + +
119A ALA* 5.4 3.8 - - + +
122A PHE* 4.8 9.4 - - + -
123A ILE* 3.9 22.9 - - + -
143A ILE* 4.4 9.6 - - + -
144A ALA 3.7 19.0 + - - +
145A VAL* 6.0 0.9 - - + -
157A ILE* 4.6 16.8 - - + -
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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