Contacts of the strand formed by residues 36 - 39 (chain I) 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 VAL 36 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6I PHE* 3.5 6.7 - - - -
8I ALA* 4.5 0.4 - - - -
10I VAL* 3.5 17.0 - - + +
12I VAL* 4.1 22.0 - - + -
26I VAL* 3.6 42.8 - - + +
29I GLN* 4.5 11.2 - - + +
30I ALA 4.6 0.4 - - - +
34I GLU* 3.8 21.5 - - + +
35I THR* 1.3 79.1 - - - +
37I ALA* 1.3 67.7 + - - +
38I VAL* 4.3 0.9 - - + -
100I SER 3.0 7.3 + - - -
101I VAL* 3.2 10.8 - - + +
102I ARG 3.0 23.2 + - - -
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Residues in contact with ALA 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I PHE* 4.3 2.7 - - + -
8I ALA* 3.9 12.1 - - + -
10I VAL 3.1 6.1 + - - +
11I ILE* 3.5 5.6 - - + +
12I VAL* 2.8 29.8 + - - +
36I VAL* 1.3 77.1 - - - +
38I VAL* 1.3 63.2 + - - +
39I VAL* 3.8 1.0 + - + -
102I ARG 3.3 7.9 - - - +
104I TYR* 4.0 11.7 - - + -
109I TYR* 3.7 31.4 - - + +
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Residues in contact with VAL 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.4 9.9 - - + +
14I ALA* 3.7 26.5 - - + +
22I VAL* 4.9 3.6 - - + -
26I VAL* 4.2 30.3 - - + -
36I VAL* 4.7 0.7 - - + -
37I ALA* 1.3 74.0 - - - +
39I VAL* 1.3 59.8 + - - +
41I ALA* 5.2 0.7 - - - -
79I PHE* 3.8 20.0 - - + -
83I ILE* 4.4 17.9 - - + -
101I VAL* 5.1 1.8 - - + -
102I ARG 2.9 8.6 + - - +
103I VAL* 3.5 16.5 - - + +
104I TYR* 2.6 35.7 + - - +
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Residues in contact with VAL 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE* 3.8 20.2 - - + -
12I VAL 2.7 16.4 + - - +
13I ASP* 4.6 4.5 - - + +
14I ALA* 2.9 28.8 + - - +
37I ALA 4.7 0.9 - - - +
38I VAL* 1.3 75.6 - - - +
40I ASN* 1.3 84.7 + - - +
41I ALA 3.3 2.5 - - - -
104I TYR* 4.0 2.2 - - + -
106I GLY 3.2 6.3 - - - +
107I ASN* 3.1 53.6 - - + +
108I PRO* 4.5 3.1 - - + -
109I TYR* 4.2 10.3 - - + -
113I GLY 5.6 1.1 - - - +
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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