Contacts of the strand formed by residues 2 - 9 (chain A) in PDB entry 3CVC
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 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLU* 1.3 83.4 - - - +
3A PHE* 1.3 66.1 + - - +
4A THR* 4.2 5.0 + - - +
28A THR* 3.2 30.0 + - + +
30A LYS* 3.9 31.4 - - + -
73A GLU* 5.8 0.2 - - + -
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Residues in contact with PHE 3 (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 GLU* 3.6 41.5 - - + -
2A THR* 1.3 75.0 - - - +
4A THR* 1.3 63.6 + - - +
5A VAL* 5.1 0.2 - - - -
21A VAL* 3.8 26.5 - - + -
22A THR 3.7 15.0 - - - -
23A VAL* 3.5 22.7 - - + -
27A ASP* 3.5 26.5 - - - -
28A THR 2.8 12.9 + - - +
29A VAL* 3.4 9.6 - - + +
30A LYS 2.8 24.3 + - - +
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Residues in contact with THR 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 THR* 4.2 5.6 + - - +
3A PHE* 1.3 74.2 - - - +
5A VAL* 1.3 69.2 + - - +
6A LYS* 4.3 10.1 + - + +
17A GLU 4.2 0.9 - - - +
18A PRO* 3.8 13.9 - - - +
21A VAL* 5.7 0.3 - - - +
30A LYS* 3.2 22.6 - - - +
32A VAL* 3.8 23.8 - - + -
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Residues in contact with VAL 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 PHE 4.7 0.9 - - - +
4A THR* 1.3 81.8 - - - +
6A LYS* 1.3 72.2 + - - +
7A MET 3.7 0.5 + - - -
16A PHE* 3.9 6.7 - - + -
17A GLU 3.6 3.4 - - - +
18A PRO* 3.7 20.6 - - + +
21A VAL* 3.7 30.5 - - + -
29A VAL* 4.0 17.0 - - + -
30A LYS 2.8 9.0 + - - +
31A TRP* 3.2 32.3 - - + +
32A VAL 2.9 23.7 + - - -
87A TYR* 3.7 10.1 - - - +
101A ILE* 6.4 0.4 - - + -
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Residues in contact with LYS 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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4A THR* 5.0 11.2 - - + +
5A VAL* 1.3 74.7 - - - +
7A MET* 1.3 61.1 + - - +
8A GLY 3.5 12.9 + - - +
10A ASP* 2.9 34.4 + - - +
15A GLN 3.6 0.2 - - - +
16A PHE* 3.4 7.1 - - - -
17A GLU* 2.9 50.7 + - + +
32A VAL* 3.5 9.0 - - + +
34A ASN* 3.5 23.9 + - + +
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Residues in contact with MET 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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6A LYS* 1.3 71.3 - - - +
8A GLY* 1.3 58.7 + - - +
16A PHE* 3.9 12.6 - - + -
31A TRP* 3.9 28.7 - - + +
32A VAL 2.8 15.4 + - - +
33A ASN* 3.6 37.0 - - + +
34A ASN 2.9 24.4 + - - -
35A LYS 3.2 7.8 + - - +
39A HIS* 3.5 30.5 + - + -
41A ILE* 4.1 11.0 - - - -
65A MET* 3.6 40.4 - - + -
70A GLU 4.4 2.5 - - - +
97A MET* 4.0 7.9 - - + -
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Residues in contact with GLY 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 LYS* 3.8 7.6 - - - +
7A MET* 1.3 70.4 - - - +
9A ALA* 1.3 62.3 + - - -
13A LEU 3.5 10.3 - - - -
15A GLN 2.8 20.5 + - - -
17A GLU* 5.3 0.2 - - - -
34A ASN* 2.8 27.6 + - - +
35A LYS 3.5 16.6 - - - -
39A HIS* 4.1 4.0 - - - -
97A MET* 3.6 5.2 - - - +
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Residues in contact with ALA 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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8A GLY* 1.3 75.7 - - - -
10A ASP* 1.3 66.2 + - - +
11A SER* 4.1 9.9 - - - +
12A GLY* 2.9 12.5 + - - -
13A LEU* 3.0 34.2 + - + +
15A GLN* 3.7 21.2 + - + +
17A GLU* 4.7 14.4 - - + -
34A ASN* 3.6 0.4 - - - -
35A LYS* 3.3 10.4 - - - +
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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