Contacts of the strand formed by residues 81 - 87 (chain D) in PDB entry 4D2W
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 LYS 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PHE* 4.6 7.1 - - - -
136A GLU* 4.8 10.0 + - - +
2D LYS* 6.1 0.4 - - - +
3D ASP* 3.9 26.8 + - + -
4D TYR* 3.3 33.9 + - - -
24D LYS* 5.8 1.2 - - - +
41D ILE* 3.9 14.9 - - + +
42D MET 3.3 8.5 - - - +
43D ASP* 3.4 26.5 - - + +
44D LYS* 3.7 2.2 - - - +
77D GLU* 3.4 9.4 - - - +
78D THR* 3.0 38.2 + - - +
79D ALA 3.7 0.4 - - - -
80D ASN* 1.4 85.6 - - - +
82D ILE* 1.4 63.4 + - - +
83D PHE* 3.6 23.3 - - + -
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Residues in contact with ILE 82 (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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40D LYS 3.6 1.6 - - - +
41D ILE* 3.8 0.7 - - - -
42D MET* 2.8 43.4 + - + +
44D LYS* 4.1 17.5 - - + -
47D LEU* 4.3 5.2 - - + -
51D LEU* 3.8 28.9 - - + -
54D ILE* 4.2 17.3 - - + -
55D LYS* 4.5 13.2 - - - +
58D ILE* 4.1 23.1 - - + -
75D VAL* 4.6 5.4 - - + -
76D LEU 3.6 7.0 - - - +
77D GLU* 4.0 18.6 - - + +
81D LYS* 1.4 76.7 - - - +
83D PHE* 1.3 72.2 + - - +
84D MET* 4.6 3.8 - - + -
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Residues in contact with PHE 83 (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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3D ASP 3.2 29.2 - - - -
4D TYR* 3.9 19.5 - + - -
7D LEU* 4.0 27.4 - - + -
39D ILE* 4.2 5.4 - - + -
40D LYS 3.4 4.7 - - - +
41D ILE* 3.7 36.6 - - + -
74D HIS 4.5 0.2 - - - -
75D VAL* 3.4 9.4 - - - +
76D LEU* 2.8 68.4 + - + +
78D THR* 4.0 10.5 - - + -
81D LYS* 3.6 25.8 - - + -
82D ILE* 1.3 74.0 - - - +
84D MET* 1.4 63.6 + - - +
85D VAL 4.1 0.7 - - - -
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Residues in contact with MET 84 (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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38D ALA 3.7 0.3 - - - +
39D ILE* 3.5 2.5 - - - -
40D LYS* 2.9 43.7 + - + +
42D MET* 4.2 27.1 - - - +
54D ILE* 4.6 2.7 - - - -
57D GLU* 4.0 28.9 - - + +
58D ILE* 3.8 41.3 - - + -
61D LEU* 5.1 3.8 - - + -
72D LEU* 4.1 21.8 - - + -
74D HIS 3.6 3.8 - - - -
75D VAL* 4.7 2.2 - - + -
82D ILE* 4.6 4.3 - - + -
83D PHE* 1.4 75.5 - - - +
85D VAL* 1.3 64.9 + - - +
86D LEU* 3.6 25.0 + - + +
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Residues in contact with VAL 85 (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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7D LEU* 4.7 0.2 - - + -
11D TYR* 3.7 33.4 - - + +
37D VAL* 3.7 37.2 - - + -
38D ALA 3.8 2.2 - - - -
39D ILE* 4.1 17.3 - - + +
72D LEU* 3.6 6.2 - - - +
73D TYR* 2.8 38.5 + - + -
74D HIS* 2.8 29.9 + - + +
76D LEU* 3.9 15.7 - - + -
84D MET* 1.3 73.3 - - - +
86D LEU* 1.3 57.1 + - - +
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Residues in contact with LEU 86 (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 VAL* 3.6 8.0 - - - +
38D ALA* 2.8 39.8 + - + +
40D LYS* 4.1 29.4 - - + +
61D LEU* 5.5 4.0 - - + -
70D CYS* 4.1 21.1 - - + +
71D GLN 3.3 16.2 - - - +
72D LEU* 3.9 23.3 - - + +
73D TYR* 3.7 5.4 - - - -
84D MET* 3.9 28.9 - - + +
85D VAL* 1.3 76.5 - - - +
87D GLU* 1.3 60.7 + - - +
88D TYR 3.5 0.5 + - - -
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Residues in contact with GLU 87 (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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38D ALA* 4.3 5.2 - - - +
66D HIS 5.2 0.3 - - - +
69D ILE 3.4 10.2 - - - +
70D CYS* 3.6 13.2 - - - -
71D GLN* 2.9 41.2 + - - +
73D TYR* 3.6 26.2 - - - +
86D LEU* 1.3 75.8 - - - +
88D TYR* 1.3 72.8 + - - +
89D CYS* 3.4 13.8 + - - -
141D ASP* 4.3 4.8 - - + +
147D LYS* 2.8 35.1 + - - -
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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