Contacts of the strand formed by residues 72 - 85 (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 SER 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E LYS* 4.3 17.8 - - - +
16E GLU* 5.1 2.8 + - - -
63E VAL* 3.0 36.1 + - - +
70E ALA 4.6 3.0 + - - -
71E ASP* 1.3 78.4 - - - +
73E LEU* 1.3 69.6 + - - +
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Residues in contact with LEU 73 (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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60E THR* 3.8 20.2 - - + -
61E VAL 3.5 22.4 - - - +
62E ARG* 4.9 3.6 - - - -
71E ASP* 6.0 1.6 - - - +
72E SER* 1.3 81.0 - - - +
74E TYR* 1.3 63.5 + - - +
75E THR* 4.2 1.7 + - - +
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Residues in contact with TYR 74 (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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39D THR 5.6 0.2 + - - -
41D LEU* 3.4 32.9 - - + +
44D LYS* 3.8 25.5 + - - +
52D ASN* 5.4 1.7 + - - -
12E ILE* 3.5 32.5 - - + -
13E GLU 5.6 2.9 - - - -
60E THR* 3.8 5.1 - - - +
61E VAL* 3.6 27.3 + - - +
63E VAL* 3.7 23.7 - - + +
73E LEU* 1.3 76.6 - - - +
75E THR* 1.3 79.5 + - - +
76E TYR* 3.7 6.2 + - + -
77E PRO* 6.2 0.2 - - + -
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Residues in contact with THR 75 (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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52D ASN* 5.7 2.3 + - - -
58E TYR* 4.3 24.4 - - + -
59E GLU 3.4 6.7 - - - +
60E THR* 3.3 25.6 - - + +
73E LEU 4.2 1.7 + - - +
74E TYR* 1.3 88.8 - - - +
76E TYR* 1.3 59.6 + - - +
77E PRO* 4.1 4.6 - - - +
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Residues in contact with TYR 76 (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* 5.4 2.9 - - + -
10E ILE* 4.1 26.2 - - + -
12E ILE* 4.3 11.4 - - + -
23E ILE* 4.6 13.4 - - + +
24E ASN 5.0 1.4 + - - -
25E THR* 3.1 29.4 + - + -
58E TYR* 4.1 2.5 - - - -
59E GLU* 2.9 75.9 + - + +
60E THR 5.0 0.2 + - - -
61E VAL* 4.1 27.5 - - + +
74E TYR* 4.2 11.0 - - + -
75E THR* 1.3 74.8 - - - +
77E PRO* 1.3 76.9 - - + +
78E VAL* 3.7 14.3 + - + +
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Residues in contact with PRO 77 (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* 4.2 10.7 - - + +
52D ASN* 4.1 35.0 - - + +
53D VAL* 4.7 2.0 - - + -
27E TRP* 3.1 26.6 + - + -
56E LEU* 3.9 24.2 - - + -
57E VAL 3.4 8.7 - - - +
58E TYR* 3.8 24.4 - - + -
74E TYR* 6.2 0.2 - - + -
75E THR 4.1 2.5 - - - +
76E TYR* 1.3 92.7 - - + +
78E VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 78 (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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25E THR* 3.4 20.0 - - + -
26E THR* 3.6 22.2 - - + +
27E TRP* 4.1 1.8 - - - +
56E LEU* 3.0 15.4 - - - +
57E VAL* 2.8 38.4 + - + +
59E GLU* 3.9 16.6 - - + -
76E TYR* 3.8 29.6 - - + +
77E PRO* 1.3 76.0 - - - +
79E ALA* 1.3 66.8 - - - +
80E THR 3.4 0.9 + - - -
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Residues in contact with ALA 79 (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* 3.4 20.6 - - + +
26E THR* 3.3 30.3 + - - +
27E TRP* 3.6 35.7 - - + -
53E PHE* 4.4 4.7 - - + -
55E GLU 3.9 0.9 - - - -
56E LEU* 3.6 8.4 - - - +
57E VAL* 5.7 0.2 - - - -
78E VAL* 1.3 74.7 - - - +
80E THR* 1.3 61.0 + - - +
81E GLN 4.8 0.2 - - - +
82E CYS* 4.0 9.6 - - - -
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Residues in contact with THR 80 (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* 3.3 18.4 - - - +
55E GLU* 2.9 27.6 + - + +
57E VAL* 3.6 35.1 + - + +
78E VAL 3.4 0.4 + - - -
79E ALA* 1.3 73.6 - - - +
81E GLN* 1.3 68.8 + - + +
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Residues in contact with GLN 81 (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* 4.2 4.5 - - + -
53E PHE* 3.1 8.3 - - - +
54E LYS* 2.5 60.4 + - + +
55E GLU* 3.5 28.6 + - + +
80E THR* 1.3 90.3 - - + +
82E CYS* 1.3 60.6 + - - +
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Residues in contact with CYS 82 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E CYS* 4.3 14.1 - - - +
4E GLU* 3.9 18.4 + - - +
5E LEU* 3.6 30.4 - - + +
28E CYS* 2.0 58.1 - - + -
52E THR 3.4 3.4 - - - +
79E ALA* 4.0 3.4 - - - -
81E GLN* 1.3 75.3 - - - +
83E HIS* 1.3 60.3 + - - +
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Residues in contact with HIS 83 (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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3E CYS* 3.2 17.5 - - - -
50E THR 3.5 0.3 - - - +
52E THR* 3.1 37.9 + - + +
53E PHE 3.9 15.9 + - - -
54E LYS* 3.9 34.6 - - + +
81E GLN 4.2 0.6 - - - -
82E CYS* 1.3 74.8 - - - +
84E CYS* 1.3 64.5 + - - +
85E GLY* 3.8 21.9 - - - -
86E LYS 5.0 2.0 + - - -
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Residues in contact with CYS 84 (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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3E CYS* 3.7 13.9 - - - +
31E TYR 3.8 1.6 - - - -
32E CYS* 2.0 53.8 - - + -
33E TYR 4.8 1.8 - - - +
49E LYS* 3.5 28.1 + - + +
50E THR 3.4 4.3 - - - -
83E HIS* 1.3 78.5 + - - +
85E GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 85 (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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49E LYS* 3.8 14.9 - - - +
50E THR* 3.0 31.6 + - - +
52E THR* 4.0 4.6 - - - +
83E HIS* 3.6 21.9 + - - -
84E CYS* 1.3 76.0 - - - +
86E LYS* 1.3 65.6 + - - -
87E CYS 3.5 1.7 + - - -
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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