Contacts of the strand formed by residues 85 - 93 (chain D) in PDB entry 2ESV
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 ALA 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D ARG* 4.1 8.7 - - - -
36D GLN 3.2 23.8 - - - +
37D ILE* 3.7 12.3 - - + +
38D HIS 5.4 1.1 - - - +
83D ASP 3.3 4.0 + - - +
84D THR* 1.3 78.0 - - - +
86D VAL* 1.3 65.0 + - - +
87D TYR* 3.4 21.9 - - + -
110D THR* 4.7 3.1 - - - -
111D LEU 2.9 29.3 + - - +
112D GLN* 6.3 0.2 - - - -
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Residues in contact with VAL 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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35D ARG* 3.2 6.1 - - - +
36D GLN* 2.9 40.0 + - + +
38D HIS 6.0 0.9 - - - +
85D ALA* 1.3 74.6 - - - +
87D TYR* 1.3 63.3 + - - +
88D TYR* 3.6 35.9 + - + +
107D GLN 3.7 18.6 - - - +
108D GLY* 4.3 1.6 - - - -
109D THR 3.4 13.2 - - - +
110D THR* 4.1 20.4 - - + +
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Residues in contact with TYR 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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7D GLN* 2.8 21.8 + - - -
19D LEU* 3.7 16.6 - - + -
33D TRP* 4.4 6.5 - - + -
34D TYR 3.7 2.2 - - - +
35D ARG* 3.0 40.7 + - + -
45D ILE* 3.7 22.4 - - + -
74D LEU* 3.7 13.7 - - + -
76D LEU* 3.4 28.0 - - + +
83D ASP* 2.5 30.9 + - - -
85D ALA* 3.4 23.3 - - + -
86D VAL* 1.3 72.9 - - - +
88D TYR* 1.3 62.6 + - - +
108D GLY* 3.2 0.3 - - - -
109D THR* 2.8 29.0 + - - +
111D LEU* 3.6 19.5 - - + -
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Residues in contact with TYR 88 (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 GLN* 4.0 1.8 - - - -
32D TYR 3.9 0.3 - - - +
33D TRP* 3.3 8.8 - - - -
34D TYR 2.8 41.8 + - - +
35D ARG* 4.5 1.6 - - - -
36D GLN* 3.6 37.2 + - + -
42D PRO* 5.8 0.2 - - + -
86D VAL* 3.6 34.7 - - + +
87D TYR* 1.3 72.3 - - - +
89D CYS* 1.3 59.7 + - - +
90D ILE* 3.9 12.4 + - + +
105D PHE* 3.6 42.0 - + + -
106D GLY 3.3 29.6 - - - +
107D GLN 3.9 4.3 - - - -
108D GLY* 3.9 9.0 - - - -
37E ARG* 3.5 24.7 + - - -
42E GLU* 5.1 0.4 - - - -
43E ILE* 4.7 3.1 - - + -
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Residues in contact with CYS 89 (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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5D THR* 3.3 25.6 + - - -
7D GLN* 3.0 25.0 + - - +
21D CYS* 2.0 48.0 - - - -
23D HIS* 4.5 0.2 - - - -
31D VAL* 4.2 14.8 - - - -
32D TYR 3.5 4.0 - - - -
33D TRP* 3.6 26.9 - - + -
88D TYR* 1.3 71.5 - - - +
90D ILE* 1.3 62.7 + - - +
104D ILE 5.3 0.7 - - - +
106D GLY* 5.5 4.0 + - - -
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Residues in contact with ILE 90 (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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5D THR* 4.7 1.3 - - - -
30D TYR 3.7 0.2 - - - +
31D VAL* 4.9 0.2 - - - -
32D TYR* 2.8 43.9 + - + +
34D TYR* 4.3 16.8 - - + -
88D TYR* 4.1 15.5 - - + +
89D CYS* 1.3 78.5 - - - +
91D VAL* 1.3 72.6 + - - +
92D VAL* 4.0 13.0 - - + -
103D LEU* 4.2 15.5 - - + -
104D ILE* 3.4 40.2 - - + +
105D PHE* 3.8 34.8 - - + -
106D GLY 5.2 0.4 - - - +
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Residues in contact with VAL 91 (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 LYS* 4.2 17.4 - - + +
5D THR* 3.7 27.9 + - + +
23D HIS* 4.0 9.6 - - + -
26D ILE* 3.9 23.3 - - + -
30D TYR* 3.3 46.0 - - + +
31D VAL* 4.0 14.1 - - + -
90D ILE* 1.3 79.3 - - - +
92D VAL* 1.3 65.6 + - - +
93D ARG 4.4 0.3 + - - -
104D ILE* 5.8 3.8 - - - +
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Residues in contact with VAL 92 (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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30D TYR* 2.8 39.9 + - - -
32D TYR* 3.4 31.9 + - + +
90D ILE* 4.0 6.3 - - + -
91D VAL* 1.3 79.0 - - - +
93D ARG* 1.3 75.1 + - - +
94D SER 3.6 0.9 + - - -
95D SER* 4.6 0.7 - - - +
98D GLY* 3.8 29.4 - - - +
102D LYS 3.9 12.3 - - - +
103D LEU* 3.7 26.0 - - + -
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Residues in contact with ARG 93 (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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62A ARG* 4.0 26.1 - - - +
4D LYS* 5.1 6.0 - - - +
25D THR 5.7 0.6 + - - -
27D SER* 3.0 24.2 + - - -
29D ASN* 3.8 24.1 + - - +
30D GLU* 3.3 40.2 + - + +
91D VAL* 4.2 1.0 + - - +
92D VAL* 1.3 80.7 - - - +
94D SER* 1.3 79.0 + - - +
95D SER* 3.1 14.5 + - - -
4P PRO* 5.6 2.0 - - + -
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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