Contacts of the strand formed by residues 36 - 42 (chain B) in PDB entry 4XJO
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY 2.9 11.4 + - - +
95A LEU* 3.2 18.1 - - + +
96A THR* 2.9 19.7 + - - -
33B VAL* 6.3 1.1 - - + -
34B SER 4.7 4.5 - - - +
35B PRO* 1.3 73.2 - - - +
37B VAL* 1.3 64.4 + - - +
38B ALA 3.3 0.9 + - - -
48B LEU* 3.7 31.2 - - + -
49B ILE 3.5 20.4 - - - +
50B ARG* 6.0 2.2 - - - -
389B THR* 5.5 2.9 - - + -
393B LEU* 4.5 21.1 - - + -
398B TRP* 4.5 7.2 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 3.6 14.4 - - + +
97A HIS* 4.9 0.7 - - - -
10B PRO* 3.8 17.7 - - + +
13B ILE* 4.0 26.0 - - + -
14B ILE* 3.7 34.1 - - + -
35B PRO 3.9 0.2 + - - -
36B VAL* 1.3 73.8 - - - +
38B ALA* 1.3 64.6 + - - +
39B VAL* 3.9 20.9 - - + -
48B LEU* 3.3 2.9 - - - -
49B ILE* 2.8 46.9 + - + +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A MET* 3.7 20.2 - - - +
90A VAL* 4.0 20.2 - - + -
95A LEU* 4.6 6.1 - - + -
96A THR 2.8 15.9 + - - +
97A HIS* 3.6 20.6 - - - +
98A GLU 4.7 1.9 + - - -
36B VAL 3.3 1.2 + - - -
37B VAL* 1.3 75.0 - - - +
39B VAL* 1.3 63.1 + - - +
40B ALA 5.1 0.7 - - - +
47B THR 3.5 5.8 - - - +
48B LEU* 3.7 18.4 - - + -
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 4.4 13.0 - - - +
87A MET* 4.2 7.0 - - - +
10B PRO* 5.0 5.6 - - + -
13B ILE* 5.7 3.1 - - + -
37B VAL* 3.9 9.8 + - + -
38B ALA* 1.3 78.4 - - - +
40B ALA* 1.3 65.9 + - + +
47B THR* 2.8 34.4 + - + +
49B ILE* 3.7 37.7 - - + -
54B PRO* 4.7 2.9 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 3.4 17.0 - - + +
87A MET* 3.8 11.0 - - - +
38B ALA* 3.8 1.1 - - - +
39B VAL* 1.3 84.7 - - + +
41B ALA* 1.3 63.6 + - - +
42B HIS* 3.8 15.0 - - + +
46B LEU* 3.6 3.5 - - - +
47B THR* 2.8 42.5 + - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL 3.0 13.5 + - - +
87A MET* 3.6 21.5 - - + +
88A ASN* 4.6 0.6 + - - +
90A VAL* 4.2 1.6 - - + -
40B ALA* 1.3 75.8 - - - +
42B HIS* 1.3 73.5 + - - +
45B TRP 3.4 6.1 - - - -
46B LEU* 3.9 15.0 - - + -
71B HIS* 3.5 37.3 - - + +
72B GLY* 4.6 1.7 + - - -
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU 5.6 0.4 - - - -
85A ARG 3.2 26.9 + - - -
86A VAL* 3.3 19.9 + - - +
40B ALA* 3.8 17.9 - - + +
41B ALA* 1.3 85.1 + - - +
43B GLY* 1.3 67.8 + - - +
44B ALA 3.3 0.3 + - - -
45B TRP* 2.9 30.3 + - + +
47B THR* 5.2 3.6 - - - -
71B HIS* 3.8 4.4 - - - +
72B GLY* 5.3 7.2 + - - -
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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