Contacts of the strand formed by residues 75 - 85 (chain D) in PDB entry 1XWD
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 LYS 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D ARG* 3.4 45.5 - - + +
68D VAL 3.4 8.1 - - - +
69D THR* 4.0 23.9 + - - +
73D GLY 4.6 5.4 - - - +
74D PHE* 1.3 78.9 - - - +
76D VAL* 1.3 63.8 + - - +
39E TYR* 4.5 10.6 - - - -
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 3.7 33.7 - - + -
25D ILE* 3.3 35.4 - - + -
67D ARG* 3.6 4.9 - - - +
68D VAL* 2.9 37.1 + - + +
70D VAL* 4.2 6.7 - - + -
74D PHE* 4.0 7.4 - - + -
75D LYS* 1.3 78.3 - - - +
77D GLU* 1.3 64.1 + - - +
78D ASN 3.9 0.2 + - - -
38E VAL* 3.5 19.3 - - + +
39E TYR* 3.8 18.6 - - + +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 3.9 0.5 - - - +
62D ALA* 5.2 0.5 - - - +
65D TYR* 3.6 47.6 - - + -
66D ASN 3.6 4.9 - - - -
67D ARG* 4.6 5.4 - - + +
76D VAL* 1.3 76.8 - - - +
78D ASN* 1.3 59.3 + - - +
79D HIS* 3.5 18.1 + - + -
36E ASP* 5.1 1.4 - - - +
37E LEU 4.3 4.7 - - - +
38E VAL* 3.0 49.6 + - - +
40E LYS* 4.0 21.8 + - - +
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Residues in contact with ASN 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 3.3 8.4 - - + -
26D LEU* 2.9 33.8 + - - +
65D TYR* 3.2 3.5 - - - -
66D ASN* 2.9 41.0 + - + +
68D VAL* 4.0 21.5 - - + +
76D VAL 3.9 1.4 + - - -
77D GLU* 1.3 71.4 - - - +
79D HIS* 1.3 63.4 + - - +
80D THR* 3.6 11.6 + - - +
93D NAG 1.5 54.7 + - - +
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Residues in contact with HIS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.2 23.0 - - + +
26D LEU* 2.8 30.6 + - - +
27D GLN* 3.3 2.8 - - - -
28D CYS* 2.8 32.6 + - - +
62D ALA* 3.4 27.9 - - + +
64D SER 3.7 3.4 - - - +
65D TYR* 3.9 13.7 - - + -
77D GLU* 3.5 24.0 + - + +
78D ASN* 1.3 77.2 + - - +
80D THR* 1.3 60.7 + - - +
93D NAG 4.9 0.7 + - - -
36E ASP* 3.5 33.7 + - + -
37E LEU 4.2 3.3 + - - -
38E VAL* 3.7 15.1 - - + +
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Residues in contact with THR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.5 20.2 - - - +
64D SER* 2.5 33.5 + - - +
65D TYR* 4.3 1.3 + - - -
66D ASN* 3.5 28.3 - - - +
78D ASN* 3.7 14.4 - - - +
79D HIS* 1.3 78.6 - - - +
81D ALA* 1.3 61.5 + - - +
93D NAG 4.7 11.2 - - - +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.3 2.9 - - - +
28D CYS* 3.3 8.8 - - - -
62D ALA* 3.5 1.2 - - - -
63D LYS* 2.7 51.6 + - - +
64D SER* 3.0 24.0 + - - +
79D HIS 3.8 0.2 - - - -
80D THR* 1.3 81.2 + - - +
82D CYS* 1.3 59.5 + - - +
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Residues in contact with CYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D CYS* 4.4 21.8 - - - +
11D THR* 3.9 12.6 - - - -
12D LEU* 3.7 24.6 - - + +
28D CYS* 2.0 54.3 - - + -
61D VAL 3.5 5.4 - - - +
63D LYS* 3.2 8.9 + - - +
81D ALA* 1.3 74.2 - - - +
83D HIS* 1.3 58.3 + - - +
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D CYS* 4.5 3.6 - - - -
61D VAL* 3.1 37.0 + - + +
62D ALA 4.4 0.6 + - - -
63D LYS* 3.3 53.1 - - + +
82D CYS* 1.3 72.9 - - - +
84D CYS* 1.3 65.4 + - - +
85D SER* 3.2 29.7 + - - -
74F LYS* 5.3 4.9 - - - -
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Residues in contact with CYS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D CYS* 3.9 13.6 - - - -
31D CYS 3.9 1.6 - - - -
32D CYS* 2.0 50.0 - - + -
58D THR* 3.2 19.9 + - + +
59D CYS 3.4 6.1 - - - -
83D HIS* 1.3 74.0 + - - +
85D SER* 1.3 57.0 + - - +
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D THR* 3.3 8.7 + - - -
59D CYS 2.8 32.1 + - - +
61D VAL* 3.8 13.2 - - - +
83D HIS* 3.2 30.9 + - - -
84D CYS* 1.3 74.2 - - - +
86D THR* 1.3 73.5 + - - +
96E VAL* 5.2 3.4 - - - -
74F LYS* 3.1 23.4 + - - -
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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