Contacts of the strand formed by residues 51 - 58 (chain A) in PDB entry 2XAC
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 CYS 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 3.6 24.5 - - + -
33A VAL 3.3 15.3 - - - +
34A PRO* 4.6 1.6 - - + -
35A LEU* 3.8 3.8 - - - -
49A PRO* 3.2 12.2 - - - +
50A SER* 1.3 80.4 - - - +
52A VAL* 1.3 63.8 + - - +
24B ALA* 3.2 30.2 - - - +
59B GLY* 3.9 1.1 - - - -
60B CYS* 2.0 57.6 - - + -
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 4.6 1.3 - - - -
33A VAL* 2.7 42.7 + - + +
34A PRO 4.5 1.8 - - - +
35A LEU* 4.4 1.8 - - + +
49A PRO* 4.8 1.1 - - + -
51A CYS* 1.3 79.5 - - - +
53A THR* 1.3 62.1 + - - +
54A VAL* 4.7 2.0 - - + -
78A MET* 3.7 18.2 - - - -
80A ILE* 3.9 4.3 - - + -
93A MET* 3.6 34.8 - - + -
95A LEU* 3.7 24.7 - - + -
20B VAL* 3.6 27.6 - - + -
23B ARG 4.9 0.2 - - - -
24B ALA* 4.4 3.4 - - - -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 3.4 34.5 - - + -
31A VAL 3.5 16.2 - - - +
32A VAL* 4.2 6.8 - - - +
52A VAL* 1.3 71.4 - - - +
54A VAL* 1.3 63.5 + - - +
78A MET* 4.4 14.0 - - - +
97A GLU* 5.0 1.2 - - - +
23B ARG* 3.0 26.2 + - + +
24B ALA* 4.1 2.6 - - - -
29B ARG* 2.7 34.7 + - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG 3.4 0.3 - - - +
30A GLU* 3.1 7.1 - - - -
31A VAL 2.8 40.4 + - - +
33A VAL* 3.8 13.0 - - + -
52A VAL* 4.7 4.3 - - + -
53A THR* 1.3 78.1 - - - +
55A GLN* 1.3 60.2 + - - +
56A ARG* 3.5 36.7 + - + +
76A VAL* 4.7 2.9 - - + -
78A MET* 5.3 2.5 - - + -
95A LEU* 3.7 39.5 - - + -
96A GLU 4.1 7.2 - - - +
97A GLU* 3.9 11.9 - - + -
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.6 31.4 + - + +
29A ARG* 3.3 15.0 - - - +
30A GLU* 4.6 0.9 - - + +
54A VAL* 1.3 71.9 - - - +
56A ARG* 1.3 64.0 + - - +
74A HIS* 5.1 2.6 - - - -
97A GLU* 3.1 25.1 + - - +
98A HIS 2.7 50.4 + - - +
99A SER* 3.8 8.8 - - - -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.8 3.6 - - - -
29A ARG* 2.8 35.5 + - - +
31A VAL* 4.7 16.1 - - + +
33A VAL* 4.3 17.4 - - - +
54A VAL* 3.5 33.2 - - + +
55A GLN* 1.3 79.3 - - - +
57A CYS* 1.3 62.2 + - - +
58A GLY* 2.9 8.1 + - - -
95A LEU* 4.5 7.3 - - - +
96A GLU* 2.7 44.8 + - - +
98A HIS* 3.6 27.4 - - + +
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Residues in contact with CYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLN 3.5 1.3 - - - -
56A ARG* 1.3 68.9 - - - +
58A GLY* 1.3 60.4 + - - +
68A CYS* 3.7 31.1 - - - +
69A VAL* 4.2 1.1 - - - -
70A PRO* 3.4 37.5 - - + -
98A HIS* 3.4 9.3 + - + +
101A CYS* 2.0 50.7 - - - -
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 3.3 0.2 - - - -
27A GLN 2.8 17.2 + - - -
29A ARG* 3.7 19.7 - - - -
31A VAL* 6.2 2.0 - - - -
56A ARG 2.9 4.8 + - - -
57A CYS* 1.3 74.0 - - - +
59A GLY* 1.3 64.6 + - - -
68A CYS* 3.1 23.0 - - - -
32B VAL* 4.3 3.8 - - - -
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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