Contacts of the strand formed by residues 59 - 69 (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 CYS 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D CYS* 3.5 8.1 - - - -
58D THR* 1.3 76.4 + - - +
60D CYS* 1.3 60.8 + - - +
61D VAL* 3.0 10.2 + - + +
84D CYS* 3.4 0.5 - - - -
85D SER 2.8 34.6 + - - +
87D CYS* 2.0 48.9 - - + -
90D HIS* 5.1 1.1 - - - -
34E THR* 4.1 12.6 - - - +
48E GLN* 3.5 38.4 - - - +
49E LYS 4.6 5.6 - - - -
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Residues in contact with CYS 60 (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* 2.0 54.3 - - + -
11D THR 4.3 0.2 - - - -
28D CYS* 4.0 6.2 - - - +
29D MET* 3.6 29.6 - - - -
30D GLY 4.2 3.8 - - - +
32D CYS* 3.3 7.9 - - - -
59D CYS* 1.3 68.6 - - - +
61D VAL* 1.3 61.1 + - - +
83D HIS 4.3 0.2 - - - -
34E THR* 3.0 31.1 + - - +
35E ARG 4.3 0.7 - - - -
36E ASP* 3.8 17.8 + - - +
48E GLN* 4.8 1.0 + - - -
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Residues in contact with VAL 61 (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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28D CYS* 3.8 5.8 - - - -
59D CYS 3.0 11.1 + - - +
60D CYS* 1.3 81.3 - - - +
62D ALA* 1.3 63.9 + - - +
63D LYS 3.5 0.2 + - - -
82D CYS* 3.5 3.3 - - - -
83D HIS* 3.1 37.0 + - - +
85D SER* 3.8 30.1 - - - +
86D THR 4.2 13.2 - - - +
36E ASP* 4.0 16.2 - - - +
48E GLN* 3.7 23.1 - - - +
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Residues in contact with ALA 62 (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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28D CYS* 3.2 13.2 - - - +
61D VAL* 1.3 76.9 - - - +
63D LYS* 1.3 64.3 + - - +
64D SER 4.5 4.3 - - - +
65D TYR* 4.7 11.3 - - + -
77D GLU* 5.2 0.4 - - - +
79D HIS* 3.4 39.9 - - + +
81D ALA 4.1 1.1 - - - +
83D HIS* 4.3 1.9 + - - -
36E ASP* 3.1 19.5 + - - +
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Residues in contact with LYS 63 (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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61D VAL 3.5 2.8 + - - -
62D ALA* 1.3 75.5 - - - +
64D SER* 1.3 60.6 + - - +
65D TYR* 4.8 5.5 - - - -
81D ALA* 2.7 25.8 + - - +
82D CYS 3.2 35.0 + - - +
83D HIS* 3.3 38.4 - - + +
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Residues in contact with SER 64 (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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62D ALA* 4.5 0.7 - - - +
63D LYS* 1.3 80.6 + - - +
65D TYR* 1.3 66.3 + - - +
79D HIS* 3.7 3.1 - - - +
80D THR* 2.5 42.8 + - - -
81D ALA* 3.0 22.2 + - - +
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Residues in contact with TYR 65 (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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62D ALA* 4.7 14.1 - - + -
63D LYS 4.8 4.7 - - - -
64D SER* 1.3 81.4 - - - +
66D ASN* 1.3 67.9 + - - +
67D ARG* 4.1 10.4 + - + -
77D GLU* 3.6 42.6 - - + -
78D ASN 3.2 15.5 - - - +
79D HIS* 3.9 12.6 - - + -
80D THR* 4.3 2.9 + - - -
123F GLN* 4.5 8.7 + - - -
145F GLN* 4.2 14.6 + - - -
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Residues in contact with ASN 66 (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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65D TYR* 1.3 75.6 - - - +
67D ARG* 1.3 59.5 + - - +
68D VAL* 3.2 22.2 + - + +
77D GLU* 3.6 1.2 - - - -
78D ASN* 2.9 37.2 + - + +
80D THR* 3.5 24.9 - - - +
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Residues in contact with ARG 67 (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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65D TYR* 4.1 12.1 + - + -
66D ASN* 1.3 71.3 - - - +
68D VAL* 1.3 59.0 + - - +
69D THR* 5.0 1.9 + - - -
75D LYS* 3.4 46.7 - - + +
76D VAL 3.7 11.0 - - - +
77D GLU* 4.6 7.0 - - + +
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Residues in contact with VAL 68 (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 19.1 - - + -
66D ASN* 3.2 28.9 + - + +
67D ARG* 1.3 74.2 - - - +
69D THR* 1.3 63.9 + - - +
75D LYS* 3.4 5.3 - - - -
76D VAL* 2.9 40.4 + - - +
78D ASN* 4.0 14.4 - - + +
93D NAG 3.9 34.1 - - + +
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Residues in contact with THR 69 (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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67D ARG 5.0 1.4 + - - -
68D VAL* 1.3 77.5 - - - +
70D VAL* 1.3 69.9 + - - +
73D GLY* 4.4 10.3 - - - +
74D PHE 3.3 16.8 - - - +
75D LYS* 4.0 25.6 + - - +
93D NAG 5.3 4.0 - - - +
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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