Contacts of the strand formed by residues 4 - 13 (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 GLU 4 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E CYS* 1.3 80.3 - - - +
5E LEU* 1.3 68.8 + - - +
6E THR* 3.4 23.6 - - + +
28E CYS* 3.5 5.5 - - - -
29E ALA 3.2 37.9 + - - +
30E GLY* 4.9 2.5 - - - -
82E CYS* 3.9 11.2 - - - +
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Residues in contact with LEU 5 (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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4E GLU* 1.3 79.5 - - - +
6E THR* 1.3 58.9 + - - +
26E THR* 3.7 16.6 - - - +
27E TRP 3.7 2.0 - - - -
79E ALA* 3.4 30.5 - - + +
80E THR 3.3 22.7 - - - +
81E GLN* 4.2 6.1 - - + -
82E CYS* 3.6 29.1 - - + +
112E NAG 4.1 14.3 - - - +
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Residues in contact with THR 6 (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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4E GLU* 3.4 35.0 - - - +
5E LEU* 1.3 75.0 - - - +
7E ASN* 1.3 71.7 + - - +
8E ILE* 3.7 7.0 + - + +
26E THR* 4.1 2.0 + - - -
27E TRP* 2.6 54.5 + - - +
29E ALA* 3.6 27.8 - - + +
112E NAG 4.8 5.8 - - - -
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Residues in contact with ASN 7 (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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6E THR* 1.3 82.6 + - - +
8E ILE* 1.3 64.3 + - - +
24E ASN* 6.0 6.2 - - + +
25E THR 3.3 8.8 - - - +
26E THR* 3.7 18.0 + - - -
112E NAG 1.5 65.1 + - - +
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Residues in contact with ILE 8 (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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37D TYR* 4.0 18.4 - - + -
6E THR* 4.5 7.4 - - - +
7E ASN* 1.3 80.2 - - - +
9E THR* 1.3 63.2 + - - +
10E ILE* 3.8 23.3 - - + -
24E ASN* 3.6 10.4 - - - +
25E THR 2.8 38.2 + - - +
27E TRP* 3.6 41.3 - - + -
28E CYS 5.8 3.4 - - - +
29E ALA* 5.8 5.2 - - + -
101E PRO* 4.8 12.8 - - + -
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Residues in contact with THR 9 (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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8E ILE* 1.3 80.0 - - - +
10E ILE* 1.3 62.2 + - - +
22E SER* 4.3 20.9 - - - +
23E ILE 3.2 5.6 - - - +
24E ASN* 3.3 20.9 + - - +
101E PRO* 3.7 4.1 - - - +
102E SER* 3.1 34.0 + - - -
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Residues in contact with ILE 10 (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* 3.5 45.8 - - + -
8E ILE* 3.8 18.1 - - + -
9E THR* 1.3 73.1 - - - +
11E ALA* 1.3 61.5 + - - +
12E ILE* 4.6 15.7 - - + -
21E ILE 3.6 0.9 - - - +
22E SER* 3.5 1.9 - - - -
23E ILE* 2.7 58.3 + - + +
25E THR* 5.0 9.0 - - - +
76E TYR* 4.1 33.7 - - + -
101E PRO* 3.5 12.6 - - + +
102E SER* 5.0 0.2 - - - -
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Residues in contact with ALA 11 (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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40D PRO* 5.3 8.8 - - - +
41D LEU 5.5 1.9 + - - -
9E THR 3.9 0.6 + - - -
10E ILE* 1.3 77.0 - - - +
12E ILE* 1.3 60.4 + - - +
13E GLU* 4.3 0.9 + - - +
20E CYS* 4.0 16.6 - - + -
21E ILE 3.4 8.7 - - - +
22E SER* 4.6 3.4 - - - +
101E PRO 3.5 8.6 + - - +
102E SER* 4.1 16.4 - - - -
103E TYR 3.8 24.8 - - - +
104E CYS* 4.8 3.6 - - + -
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Residues in contact with ILE 12 (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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41D LEU* 5.8 1.8 - - + -
10E ILE* 4.0 9.4 + - + -
11E ALA* 1.3 73.8 - - - +
13E GLU* 1.3 67.7 + - - +
20E CYS* 3.0 23.0 - - - +
21E ILE* 3.2 39.2 + - + +
23E ILE* 4.5 9.9 - - + -
61E VAL* 4.2 16.4 - - + -
63E VAL* 4.8 16.6 - - + -
74E TYR* 3.5 44.9 - - + +
76E TYR* 4.3 17.9 - - + -
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Residues in contact with GLU 13 (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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41D LEU* 3.7 53.6 - - + +
42D ARG* 4.5 12.7 + - - +
11E ALA 4.3 0.8 + - - +
12E ILE* 1.3 84.1 - - - +
14E LYS* 1.3 63.3 + - - +
15E GLU* 4.6 12.8 - - - +
19E PHE 3.9 7.9 - - - +
20E CYS* 3.7 23.3 - - - -
63E VAL* 5.3 2.6 - - - +
74E TYR* 5.6 3.3 - - - -
103E TYR 5.2 1.7 - - - +
104E CYS* 4.9 0.2 - - - -
105E SER* 2.6 31.6 + - - -
106E PHE* 3.7 8.6 - - + -
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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