Contacts of the strand formed by residues 20 - 35 (chain E) 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 20 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E ALA* 4.0 15.0 - - + -
12E ILE 3.0 18.2 - - - +
13E GLU* 3.7 22.4 - - - -
19E PHE* 1.3 79.7 - - - +
21E ILE* 1.3 63.2 + - - +
22E SER* 4.1 1.0 + - - -
103E TYR 4.4 2.5 - - - -
104E CYS* 2.0 58.5 - - + -
106E PHE* 4.0 2.5 - - - -
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Residues in contact with ILE 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ILE 3.6 0.5 - - - +
11E ALA* 3.4 4.0 - - - -
12E ILE* 3.2 47.0 + - + +
19E PHE* 4.4 21.1 - - + -
20E CYS* 1.3 77.3 - - - +
22E SER* 1.3 66.2 + - - +
23E ILE* 3.6 18.5 + - + +
61E VAL* 5.0 2.9 - - + -
62E ARG* 3.7 24.7 - - + +
63E VAL* 5.4 0.9 - - + -
64E PRO* 4.9 11.7 - - + -
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Residues in contact with SER 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E THR* 4.3 18.1 - - - +
10E ILE 3.6 6.3 - - - -
11E ALA* 4.6 3.9 - - - +
20E CYS 4.1 1.4 + - - -
21E ILE* 1.3 78.4 - - - +
23E ILE* 1.3 64.9 + - - +
102E SER* 6.2 0.3 - - - -
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Residues in contact with ILE 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E THR* 3.2 4.3 - - - +
10E ILE* 2.7 49.5 + - + +
12E ILE* 4.5 15.7 - - + -
21E ILE* 4.3 18.8 - - + +
22E SER* 1.3 77.1 - - - +
24E ASN* 1.3 83.9 + - - +
25E THR* 3.8 11.7 - - - +
61E VAL* 3.6 42.8 - - + -
76E TYR* 4.6 13.0 - - + +
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Residues in contact with ASN 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ASN* 6.0 7.0 - - + +
8E ILE 3.6 7.0 - - - +
9E THR* 3.3 18.5 + - - +
23E ILE* 1.3 86.1 - - - +
25E THR* 1.3 67.7 + - - +
76E TYR* 5.0 1.9 + - - -
112E NAG 5.4 8.1 + - - +
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Residues in contact with THR 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PRO* 5.7 0.2 - - + -
7E ASN* 3.3 7.5 - - - +
8E ILE* 2.8 38.8 + - - +
10E ILE* 5.0 12.3 - - + -
23E ILE* 3.8 6.7 - - - +
24E ASN* 1.3 79.2 + - - +
26E THR* 1.3 73.6 + - - +
27E TRP* 3.8 16.2 - - + +
76E TYR* 3.1 33.6 + - + -
78E VAL* 3.4 27.6 - - + -
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Residues in contact with THR 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 3.7 25.1 - - - +
6E THR 3.5 7.2 + - - -
7E ASN* 3.7 14.8 - - - -
25E THR* 1.3 74.4 - - - +
27E TRP* 1.3 74.9 + - - +
78E VAL* 3.6 18.5 - - + +
79E ALA* 3.3 21.8 + - - +
112E NAG 5.7 4.7 - - - -
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Residues in contact with TRP 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ALA* 3.4 33.7 - - + +
38D PRO* 3.5 26.8 - - + +
53D VAL* 3.4 36.1 - - + -
5E LEU* 4.5 0.7 - - - -
6E THR* 2.6 44.1 + - - +
8E ILE* 3.6 24.0 - - + +
25E THR* 3.8 10.5 + - + +
26E THR* 1.3 85.9 + - - +
28E CYS* 1.3 72.7 + - - +
53E PHE* 3.6 23.6 - + + -
56E LEU* 3.5 26.2 - - + -
77E PRO* 3.1 36.9 + - + -
78E VAL* 4.1 0.4 - - - +
79E ALA* 3.6 16.0 - - + +
82E CYS* 4.1 5.4 - - - -
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Residues in contact with CYS 28 (chain E).
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* 3.5 1.6 - - - +
36D ALA* 3.1 32.4 + - + +
4E GLU 3.5 2.5 - - - -
8E ILE* 5.8 1.7 - - - +
27E TRP* 1.3 83.5 - - - +
29E ALA* 1.3 65.7 + - - +
51E CYS* 3.9 14.1 - - - -
52E THR* 3.0 37.5 - - - +
53E PHE* 3.2 10.1 - - - -
82E CYS* 2.0 43.1 - - - -
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Residues in contact with ALA 29 (chain E).
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* 4.1 10.5 - - + -
34D SER 3.6 10.5 - - - -
35D ARG* 3.8 12.8 - - + -
4E GLU* 3.2 33.4 + - - +
6E THR* 3.6 17.6 - - + +
8E ILE* 5.8 6.1 - - + -
28E CYS* 1.3 79.1 - - - +
30E GLY* 1.3 58.3 + - - +
51E CYS* 3.6 6.1 - - - -
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Residues in contact with GLY 30 (chain E).
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* 3.4 15.6 - - - -
34D SER* 3.0 34.1 + - - +
3E CYS* 3.7 10.5 - - - -
4E GLU* 4.9 2.9 - - - -
29E ALA* 1.3 76.0 - - - +
31E TYR* 1.3 70.4 + - - -
51E CYS* 4.0 1.7 - - - +
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Residues in contact with TYR 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D CYS* 3.8 29.2 - - + -
31D CYS* 4.3 8.5 - - + -
32D CYS* 3.4 28.3 - - - -
33D PHE* 3.7 35.9 - + + +
3E CYS* 2.8 27.9 + - - +
30E GLY* 1.3 78.6 - - - -
32E CYS* 1.3 67.5 + - - +
84E CYS* 3.8 2.4 - - - -
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Residues in contact with CYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D CYS* 4.4 1.3 - - - -
30D GLY 3.8 0.2 - - - +
31D CYS* 3.4 23.5 - - - -
32D CYS 3.3 11.9 + - - +
34D SER* 4.6 2.7 + - - +
3E CYS* 4.0 1.8 - - - -
30E GLY 4.3 0.2 + - - -
31E TYR* 1.3 76.4 - - - +
33E TYR* 1.3 62.3 + - - +
34E THR* 3.9 5.7 + - + +
49E LYS* 3.9 19.3 - - + +
50E THR* 3.5 4.0 - - - -
51E CYS* 3.5 30.5 - - - +
84E CYS* 2.0 49.6 - - + -
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Residues in contact with TYR 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D CYS* 4.4 2.3 - - - -
8D PRO* 4.4 21.3 - - + -
29D MET* 2.8 32.7 - - - +
30D GLY* 3.3 38.1 - - - -
31D CYS* 3.9 12.7 - - - -
32E CYS* 1.3 70.1 - - - +
34E THR* 1.3 78.0 + - - +
35E ARG* 4.5 17.3 - - - -
49E LYS* 4.7 14.1 + - - +
84E CYS* 4.8 2.6 - - - +
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Residues in contact with THR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D MET* 3.6 1.7 - - - -
30D GLY 3.0 29.5 + - - +
32D CYS* 5.3 2.4 + - + +
58D THR 5.3 1.1 - - - +
59D CYS* 4.0 15.1 - - - +
60D CYS* 3.0 32.8 + - - +
32E CYS* 4.1 9.0 - - + +
33E TYR* 1.3 85.2 - - - +
35E ARG* 1.3 61.4 + - - +
47E ILE 6.0 0.4 - - - -
48E GLN* 4.6 17.3 - - - +
49E LYS 3.7 27.8 - - - +
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Residues in contact with ARG 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ASN* 6.0 2.2 - - - +
17D PHE* 6.0 3.8 - - - -
27D GLN* 4.0 18.0 + - - +
28D CYS 3.5 4.0 - - - +
29D MET* 3.4 26.7 - - + +
60D CYS 4.3 3.8 - - - -
33E TYR* 4.5 15.2 - - + -
34E THR* 1.3 76.6 - - - +
36E ASP* 1.3 51.9 + - - +
37E LEU* 4.2 25.2 - - + +
46E LYS* 2.6 31.9 + - - +
47E ILE 5.3 1.3 + - - +
48E GLN* 5.1 2.8 + - - +
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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