Contacts of the strand formed by residues 18 - 22 (chain G) in PDB entry 3CJC
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 GLN 18 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G LYS* 3.2 29.5 + - - +
11G ALA* 3.5 8.8 - - - +
12G GLY* 3.2 21.9 + - - +
13G LYS 5.4 0.4 - - - +
14G GLU 5.9 2.9 - - - -
17G LEU* 1.3 82.8 - - - +
19G ILE* 1.3 63.7 + - - +
20G TRP* 3.5 28.1 - - + -
35G TYR* 3.5 4.3 - - - +
46G ILE* 3.4 6.9 - - - +
47G LEU* 3.0 41.0 + - - +
49G THR* 4.5 4.4 + - - -
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Residues in contact with ILE 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G LEU* 3.5 17.5 - - + -
18G GLN* 1.3 78.5 - - - +
20G TRP* 1.3 75.7 + - - +
29G PRO* 3.6 3.3 - - - +
30G VAL* 3.2 37.1 + - + +
35G TYR* 3.2 53.4 + - + -
38G PHE* 4.6 8.7 - - + -
44G TYR* 4.3 13.0 - - + -
45G VAL 3.6 8.3 - - - +
46G ILE* 3.9 16.8 - - + -
110G PHE* 4.3 17.5 - - + -
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Residues in contact with TRP 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G GLU* 3.4 40.3 + - + +
10G LYS* 5.8 1.3 - - + -
11G ALA* 3.8 24.0 - - + -
18G GLN* 3.5 48.7 - - + -
19G ILE* 1.3 81.4 + - - +
21G ARG* 1.3 61.8 + - - +
22G VAL 4.2 0.2 + - - -
27G LEU* 3.7 30.7 - - + +
28G VAL 3.4 8.7 - - - +
29G PRO* 3.6 30.1 - - + +
30G VAL* 4.5 0.4 - - - -
44G TYR* 3.6 3.3 - - - +
45G VAL* 2.9 60.9 + - + +
46G ILE 4.8 0.9 - - - -
47G LEU* 4.0 17.9 - - + -
61G LEU* 6.2 0.2 - - + -
84G LEU* 5.6 8.3 - - + -
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Residues in contact with ARG 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G TRP* 1.3 73.8 - - - +
22G VAL* 1.3 69.1 + - - +
23G GLU* 3.2 44.1 + - - +
26G ASP 3.5 1.2 - - - +
27G LEU* 3.7 2.4 - - - -
28G VAL 3.1 26.7 + - - +
30G VAL* 4.2 9.7 - - + +
39G PHE* 3.3 34.4 - - - -
42G ASP* 3.4 21.7 + - + -
43G ALA 3.9 7.4 - - - +
44G TYR* 3.2 39.5 + - + -
120G GLY* 4.6 0.2 - - - -
121G VAL* 4.0 19.3 - - - +
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Residues in contact with VAL 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ARG* 1.3 72.9 - - - +
23G GLU* 1.3 59.4 + - - +
24G LYS 4.8 0.2 - - - +
25G PHE 4.6 11.9 - - - +
26G ASP 3.8 4.7 - - - +
27G LEU* 4.5 6.1 - - + -
42G ASP* 4.7 0.5 - - - +
43G ALA 3.0 26.6 + - - +
45G VAL* 4.7 4.3 - - + -
73G GLU* 3.5 47.8 - - + +
76G ALA* 3.7 22.9 - - + -
77G ALA* 4.2 16.8 - - + +
80G PHE* 4.4 16.4 - - + -
121G VAL* 3.8 7.1 - - - +
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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