Contacts of the strand formed by residues 31 - 34 (chain T) in PDB entry 3J45
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 31 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T PRO* 4.9 0.2 - - - +
15T HIS* 3.1 30.9 + - + +
16T VAL* 5.5 0.5 - - - +
20T ALA 4.3 0.2 - - - +
21T SER* 3.6 25.4 - - - +
24T MET 3.6 13.7 - - - +
25T GLU* 5.0 3.5 - - + +
30T ILE* 1.3 85.7 - - - +
32T LEU* 1.4 78.3 + - - +
82T LYS* 3.6 31.0 - - + -
83T ALA 3.5 14.4 - - - +
84T TYR* 3.6 22.4 - - + -
85T VAL* 4.9 0.7 - - - -
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Residues in contact with LEU 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T LEU* 3.7 38.6 - - + -
14T PRO* 3.7 24.7 - - + -
15T HIS* 3.7 9.6 - - - +
30T ILE* 5.1 11.7 - - + -
31T VAL* 1.4 87.7 - - - +
33T LYS* 1.3 62.7 + - - +
34T VAL* 3.8 5.6 + - + +
43T ILE* 5.8 0.9 - - + -
47T VAL* 4.3 13.0 - - + -
51T PHE* 5.6 3.8 - - + -
82T LYS* 4.3 2.3 - - - -
83T ALA* 3.5 26.2 + - - +
85T VAL* 4.2 21.1 - - + +
95T PHE* 6.4 0.4 - - + -
30Y MET* 4.2 10.1 - - + -
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Residues in contact with LYS 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T VAL 4.5 2.4 - - - +
11T LEU* 4.1 10.0 - - - +
12T ARG* 4.7 2.3 + - - +
13T ALA* 3.1 35.6 + - + +
14T PRO 3.4 20.0 - - - +
15T HIS* 4.7 5.6 - - + -
32T LEU* 1.3 73.4 - - - +
34T VAL* 1.4 64.1 + - - +
35T ALA* 3.9 18.9 + - + +
66T LYS* 5.3 6.7 - - - +
79T ASP 5.4 0.2 + - - -
80T TRP* 3.6 51.8 - - + +
81T LYS 4.0 3.6 - - - +
82T LYS* 5.4 0.4 - - - +
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Residues in contact with VAL 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T VAL 4.2 6.5 - - - +
11T LEU* 5.3 3.6 - - + -
32T LEU* 3.9 6.1 - - + +
33T LYS* 1.4 72.1 - - - +
35T ALA* 1.4 60.6 + - - +
37T ASP* 3.5 33.9 - - + +
38T ALA 5.2 0.4 - - - +
39T THR 4.9 5.2 - - - +
43T ILE* 4.1 31.0 - - + -
81T LYS* 3.2 45.2 + - + +
83T ALA* 3.8 29.4 - - + -
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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