Contacts of the strand formed by residues 26 - 38 (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 LEU 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.8 33.2 - - + -
13D GLN* 3.3 13.7 - - - +
14D GLU* 5.0 3.4 - - + -
24D PRO* 4.6 5.8 - - + +
25D ILE* 1.3 82.0 - - - +
27D GLN* 1.3 60.4 + - - +
78D ASN* 2.9 19.5 + - - +
79D HIS* 2.8 43.5 + - - +
93D NAG 3.6 35.0 - - - +
38E VAL* 3.5 8.4 - - - +
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Residues in contact with GLN 27 (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* 4.7 1.6 - - - -
13D GLN* 2.7 37.5 + - - +
15D ASN* 3.7 31.8 + - + +
18D PHE* 6.0 0.4 - - - -
25D ILE 4.3 0.2 + - - -
26D LEU* 1.3 74.3 - - - +
28D CYS* 1.3 64.3 + - - +
29D MET* 3.0 34.7 + - + +
79D HIS* 3.3 2.5 - - - -
35E ARG* 4.0 17.3 + - - +
36E ASP 2.9 25.8 - - - +
37E LEU* 3.7 15.4 - - - +
38E VAL* 3.2 33.0 - - + +
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Residues in contact with CYS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D THR 3.8 0.2 - - - -
27D GLN* 1.3 69.2 - - - +
29D MET* 1.3 59.7 + - - +
60D CYS* 4.0 6.5 - - - +
61D VAL 3.9 4.7 - - - -
62D ALA* 3.2 41.1 - - - +
79D HIS* 2.8 19.9 + - - +
81D ALA 3.3 4.7 - - - -
82D CYS* 2.0 51.6 - - + -
35E ARG* 3.5 0.7 - - - +
36E ASP* 2.8 33.3 + - + +
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Residues in contact with MET 29 (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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9D GLU 3.6 2.3 - - - +
11D THR* 2.9 29.5 + - - +
13D GLN* 3.8 32.2 - - + +
14D GLU 4.7 9.0 - - - +
15D ASN* 5.2 6.3 - - - +
16D PRO* 6.2 0.7 - - + -
27D GLN* 3.0 37.7 + - + +
28D CYS* 1.3 75.5 - - - +
30D GLY* 1.3 59.0 + - - +
60D CYS* 3.6 7.9 - - - -
33E TYR* 2.8 24.7 - - - +
34E THR 3.6 4.9 - - - +
35E ARG* 3.4 27.1 - - + +
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Residues in contact with GLY 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 5.0 0.9 - - - -
9D GLU 3.7 6.7 - - - -
10D CYS* 3.5 11.4 - - - -
29D MET* 1.3 77.2 - - - +
31D CYS* 1.3 64.3 + - - -
60D CYS* 3.8 2.9 - - - +
33E TYR* 3.3 21.6 - - - -
34E THR 3.0 34.1 + - - +
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Residues in contact with CYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D CYS* 2.0 50.7 - - + -
8D PRO* 3.2 30.7 - - - +
9D GLU* 3.7 2.9 - - - +
10D CYS* 3.3 26.4 + - - +
30D GLY* 1.3 79.6 - - - -
32D CYS* 1.3 62.9 + - - +
84D CYS* 3.9 2.1 - - - -
31E TYR* 4.3 12.3 - - + -
32E CYS 3.4 7.0 - - - +
33E TYR* 3.9 8.3 - - - -
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Residues in contact with CYS 32 (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 0.2 - - - -
31D CYS* 1.3 77.0 - - - +
33D PHE* 1.3 62.7 + - - +
34D SER* 4.8 1.2 + - - -
58D THR* 3.5 23.7 - - + +
59D CYS* 3.5 2.0 - - - -
60D CYS* 3.3 31.6 - - - -
84D CYS* 2.0 49.1 - - - -
31E TYR* 3.4 11.5 - - - -
32E CYS* 3.3 28.2 + - - +
34E THR* 5.7 2.2 + - + +
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Residues in contact with PHE 33 (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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32D CYS* 1.3 74.5 - - - +
34D SER* 1.3 76.2 + - - +
35D ARG* 4.0 27.8 - - - -
56D GLU* 5.9 0.9 - - - -
57D SER* 4.3 0.3 - - - -
58D THR* 2.7 36.2 + - + +
29E ALA* 4.1 13.2 - - + -
30E GLY* 3.4 36.3 - - - -
31E TYR* 3.7 34.9 - + + +
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Residues in contact with SER 34 (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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32D CYS 4.8 0.7 + - - -
33D PHE* 1.3 84.7 - - - +
35D ARG* 1.3 62.4 + - - +
56D GLU 3.4 15.3 - - - -
57D SER* 3.6 18.4 - - - -
58D THR 4.3 2.7 - - - -
30E GLY 3.0 31.4 + - - +
32E CYS* 4.6 5.2 - - - +
50E THR* 3.6 6.5 - - - +
51E CYS* 2.7 38.0 + - - +
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Residues in contact with ARG 35 (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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33D PHE* 4.0 20.9 - - + -
34D SER* 1.3 75.6 - - - +
36D ALA* 1.3 62.9 + - - +
37D TYR* 3.3 27.9 - - + -
55D SER* 3.5 6.4 + - - -
56D GLU* 2.9 63.3 + - + +
28E CYS 3.5 14.8 - - - +
29E ALA* 3.8 11.7 - - + +
51E CYS 3.8 7.5 - - - +
97E ARG* 5.4 7.2 - - - +
100E GLY* 4.1 5.1 - - - -
101E PRO* 3.6 32.3 - - - +
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Residues in contact with ALA 36 (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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35D ARG* 1.3 76.5 - - - +
37D TYR* 1.3 64.7 + - - +
53D VAL* 4.3 5.8 - - + -
54D THR 3.5 7.9 - - - +
55D SER* 4.7 4.0 - - - -
8E ILE* 4.7 1.0 - - - +
27E TRP* 3.4 40.0 - - + +
28E CYS* 3.1 27.1 + - + +
51E CYS 4.1 7.6 + - - +
52E THR* 4.2 13.2 - - - +
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Residues in contact with TYR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 3.3 43.1 - - + -
36D ALA* 1.3 74.6 - - - +
38D PRO* 1.3 87.0 - - + +
40D PRO* 4.1 5.6 - - + -
53D VAL* 3.7 6.6 - - - +
54D THR* 2.8 53.5 + - + +
56D GLU* 3.0 25.6 + - + -
8E ILE* 4.0 13.7 - - + -
27E TRP* 4.3 3.1 - - - -
98E GLY* 3.3 13.5 - - - -
99E LEU 5.0 0.2 - - - -
100E GLY 3.2 33.6 + - - -
101E PRO* 3.9 22.0 - - + -
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Residues in contact with PRO 38 (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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37D TYR* 1.3 94.6 - - + +
39D THR* 1.3 66.9 + - - +
40D PRO* 3.1 10.9 - - - +
52D ASN 3.8 8.3 - - - +
53D VAL* 4.8 0.7 - - - -
10E ILE* 3.5 45.7 - - + +
25E THR* 5.7 0.2 - - + -
27E TRP* 3.5 30.5 - - + +
76E TYR* 5.4 3.8 - - + -
77E PRO* 4.2 17.3 - - + +
101E PRO 4.8 4.9 - - - +
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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