Contacts of the strand formed by residues 8 - 13 (chain W) in PDB entry 1JJ2
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 ARG 8 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29040 U 3.3 47.4 + - - -
29050 A 4.9 3.0 + - - -
7W GLU* 1.3 86.7 + - - +
9W VAL* 1.3 66.7 + - - +
10W VAL* 3.6 26.7 - - + +
40W HIS* 3.8 17.8 + - - +
41W PHE* 3.6 29.6 - - + +
72W VAL 3.9 0.7 - - - +
73W ARG* 3.6 2.5 - - - +
74W ALA* 3.0 28.4 + - - +
76W ARG* 6.2 0.4 - - - +
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Residues in contact with VAL 9 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W ARG* 1.3 79.1 - - - +
10W VAL* 1.3 68.4 + - - +
11W THR* 5.7 1.1 - - - +
71W ARG* 5.0 6.3 - - + -
73W ARG* 4.0 24.7 - - + +
88W GLU* 2.9 39.7 - - - +
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Residues in contact with VAL 10 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28560 A 6.1 0.4 - - - +
8W ARG* 3.6 30.3 - - + +
9W VAL* 1.3 81.8 - - - +
11W THR* 1.3 68.4 + - - +
12W ILE* 3.5 9.5 + - + -
36W HIS* 3.4 32.3 - - + +
37W LEU* 5.3 0.4 - - + -
40W HIS* 5.7 4.3 - - + -
41W PHE* 4.3 14.8 - - + -
70W ILE 3.7 0.9 - - - +
71W ARG* 3.5 1.4 - - - -
72W VAL* 2.7 48.1 + - + +
88W GLU* 4.2 0.2 - - - +
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Residues in contact with THR 11 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28550 G 4.8 0.2 + - - -
28560 A 3.5 49.0 + - - +
28570 C 3.8 13.4 + - - +
9W VAL* 5.7 1.4 - - - +
10W VAL* 1.3 81.0 - - - +
12W ILE* 1.3 62.8 + - - +
13W PRO* 3.5 10.2 - - - +
36W HIS* 4.3 1.9 + - - -
69W LYS* 4.1 26.2 - - + -
70W ILE 3.8 4.9 - - - +
71W ARG* 3.9 22.7 + - + +
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Residues in contact with ILE 12 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W VAL* 3.5 13.9 - - + +
11W THR* 1.3 73.4 - - - +
13W PRO* 1.3 71.1 - - + +
14W LEU* 3.8 11.3 - - + +
32W LEU* 4.7 2.0 - - + +
33W ILE* 4.4 15.7 - - + -
36W HIS* 3.0 62.1 - - + +
37W LEU* 4.4 5.6 - - + -
69W LYS* 3.3 6.2 - - - -
70W ILE* 3.0 49.6 + - + +
72W VAL* 4.0 23.8 - - + -
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Residues in contact with PRO 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28550 G 3.8 25.1 - - - +
28560 A 3.6 23.1 - - - +
11W THR* 3.5 9.0 - - + +
12W ILE* 1.3 91.2 - - + +
14W LEU* 1.3 66.2 + - - +
15W ARG* 3.5 20.0 + - + +
16W ASP* 5.1 1.6 + - - +
32W LEU* 4.8 5.7 - - - +
36W HIS* 3.9 16.2 - - + +
68W SER 3.8 4.9 - - - +
69W LYS* 4.7 6.5 - - + -
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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
------------------------------------------------------------
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