Contacts of the strand formed by residues 77 - 86 (chain D) in PDB entry 3D87
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 HIS 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D ASP* 3.7 31.4 + - + +
27D THR 4.9 2.1 - - - +
38D TRP* 5.6 0.2 - - - -
65D GLN* 3.5 24.8 + - - +
66D TYR 3.0 14.4 - - - +
67D THR* 3.9 13.6 + - + +
68D CYS* 4.5 3.8 - - - -
74D VAL* 4.1 22.0 - - + +
75D LEU 5.7 0.4 + - - -
76D SER* 1.3 90.9 + - - +
78D SER* 1.3 73.5 + - - +
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Residues in contact with SER 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ASP 3.0 10.3 + - - -
9D TYR* 3.2 24.5 + - - -
26D LEU* 4.3 27.9 - - - +
27D THR 4.3 13.3 + - - -
38D TRP* 5.2 2.7 - - - -
65D GLN* 3.3 2.9 - - - -
66D TYR* 2.6 36.1 + - - +
77D HIS* 1.3 83.3 + - - +
79D LEU* 1.3 60.9 + - - +
80D LEU* 3.7 1.7 + - - -
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ASP 2.5 7.9 + - - +
8D VAL* 3.4 36.0 - - + +
9D TYR* 2.6 35.3 + - - +
41D ASP* 4.7 1.8 - - - +
64D GLY* 2.8 25.8 - - - +
65D GLN* 3.2 40.1 + - + +
78D SER* 1.3 72.3 - - - +
80D LEU* 1.3 59.1 + - - +
81D LEU* 3.8 17.2 + - + -
195D LYS 5.6 2.2 - - - +
196D LEU* 4.8 5.6 - - + -
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Residues in contact with LEU 80 (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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1D ILE* 4.0 13.7 - - + -
9D TYR* 3.7 30.5 - - + -
11D VAL* 4.3 7.9 - - + -
24D VAL* 3.4 29.4 - - + -
26D LEU* 3.9 18.4 - - + -
55D ILE* 4.7 1.3 - - + -
57D VAL* 3.8 22.2 - - + -
63D ALA* 3.3 13.0 - - + +
64D GLY* 2.5 41.5 + - - +
66D TYR* 4.3 17.7 - - + -
78D SER 3.7 1.5 + - - +
79D LEU* 1.3 73.4 - - - +
81D LEU* 1.3 67.0 + - - +
196D LEU* 4.0 1.0 - - - +
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Residues in contact with LEU 81 (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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4D LEU* 4.1 11.9 - - + -
8D VAL* 3.6 29.6 - - + -
9D TYR 2.7 15.5 + - - +
10D VAL* 3.9 14.1 - - + -
11D VAL* 2.8 31.2 + - - +
79D LEU* 4.5 10.8 - - + +
80D LEU* 1.3 79.9 - - - +
82D LEU* 1.3 63.7 + - - +
193D VAL* 3.4 25.6 - - + -
195D LYS 3.3 26.0 - - - +
196D LEU* 3.3 20.6 - - + +
198D TYR* 4.4 4.3 - - + -
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Residues in contact with LEU 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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11D VAL* 3.7 7.2 - - + -
13D LEU* 3.0 31.2 - - + -
57D VAL* 3.3 19.3 - - + -
59D GLU* 3.2 16.4 - - - +
60D PHE* 3.2 57.3 - - + +
63D ALA* 3.5 12.6 - - + -
80D LEU 5.8 0.2 - - - -
81D LEU* 1.3 83.3 - - - +
83D HIS* 1.3 59.2 + - - +
84D LYS* 3.9 8.0 + - + +
196D LEU 2.8 7.9 + - - -
197D LYS* 3.5 4.7 - - - +
198D TYR* 3.0 27.5 + - - +
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Residues in contact with HIS 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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10D VAL* 3.7 14.4 - - + -
11D VAL 3.1 14.1 + - - +
12D GLU* 2.8 34.2 + - - -
13D LEU* 3.1 25.2 + - - +
82D LEU* 1.3 73.9 - - - +
84D LYS* 1.3 60.9 + - - +
90D TRP* 2.9 53.8 - + + +
91D SER 5.4 0.2 - - - -
198D TYR* 3.4 37.6 - + + +
199D GLU* 4.7 7.2 - - + -
200D GLN* 4.9 6.5 + - + +
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Residues in contact with LYS 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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13D LEU* 3.9 4.7 - - + -
16D TYR* 2.9 66.3 + - + -
59D GLU* 4.7 1.5 + - - +
60D PHE* 3.2 36.5 - - + -
82D LEU* 4.1 13.7 + - + -
83D HIS* 1.3 76.0 - - - +
85D LYS* 1.3 59.2 + - - +
86D GLU* 3.9 13.4 + - - +
90D TRP* 3.4 6.3 - - - -
91D SER* 3.2 35.5 + - - +
93D ASP* 6.0 1.1 - - - -
197D LYS* 5.6 8.1 - - + +
198D TYR 4.9 0.8 + - - -
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Residues in contact with LYS 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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13D LEU 3.1 18.4 + - - +
14D ASP* 3.3 24.4 - - + +
15D TRP 4.4 0.2 - - - -
16D TYR* 3.1 26.3 + - - +
84D LYS* 1.3 71.1 - - - +
86D GLU* 1.3 60.0 + - - +
87D ASP 4.1 0.2 + - - -
88D GLY* 3.0 39.4 + - - +
89D ILE* 3.7 11.4 - - - +
90D TRP* 3.3 48.7 - - + +
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Residues in contact with GLU 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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16D TYR* 4.2 27.8 - - + -
84D LYS* 3.9 14.2 + - - +
85D LYS* 1.3 74.0 - - - +
87D ASP* 1.3 72.6 + - + +
88D GLY 3.0 2.5 - - - -
89D ILE* 2.8 46.1 + - + +
91D SER* 4.0 25.8 - - - -
93D ASP* 4.7 7.6 - - - +
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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