Contacts of the strand formed by residues 87 - 95 (chain A) in PDB entry 2DS4
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 GLY 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASP* 5.7 3.1 - - - -
85A GLU 3.9 0.6 + - - -
86A PRO* 1.3 76.0 - - - +
88A VAL* 1.3 57.5 + - - -
89A TYR* 4.3 4.7 - - - -
107A VAL 3.6 0.2 - - - +
108A THR* 3.5 7.1 - - - +
109A VAL* 2.6 45.0 + - - +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PRO* 3.7 2.6 - - - +
58A LYS* 3.1 44.9 + - + -
59A ASP* 3.9 15.4 + - - +
87A GLY* 1.3 73.0 - - - +
89A TYR* 1.3 68.7 + - - +
106A THR* 3.0 36.6 - - + -
107A VAL 3.3 7.2 - - - +
108A THR* 4.6 6.5 - - + +
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.7 16.2 - - + -
56A VAL 3.6 4.7 - - - -
57A PRO* 3.5 30.2 - - + +
58A LYS 4.2 0.4 - - - +
65A VAL* 3.2 35.7 - - + -
81A TYR* 6.5 0.2 - - + -
83A PRO* 4.3 8.7 - - + -
84A LYS* 4.2 2.1 + - - +
85A GLU* 2.5 47.7 + - - +
86A PRO 4.5 1.2 + - - -
87A GLY* 4.4 6.5 - - - -
88A VAL* 1.3 81.5 - - - +
90A THR* 1.3 63.8 + - - +
91A VAL 4.1 0.7 - - - -
106A THR* 3.3 9.8 - - - +
107A VAL* 2.8 41.5 + - + +
109A VAL* 3.5 25.6 - - + -
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.5 2.0 - - - -
56A VAL* 2.8 37.5 + - - -
58A LYS* 4.5 20.3 + - - +
89A TYR* 1.3 77.5 + - - +
91A VAL* 1.3 59.0 + - - +
92A TRP* 3.3 32.4 - - + +
104A PRO* 4.3 11.4 - - + -
105A PHE 3.5 15.3 - - - +
106A THR* 5.0 2.9 - - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 4.6 12.1 - - + -
53A VAL* 4.9 3.8 - - + -
54A ALA 3.8 2.5 - - - -
55A VAL* 4.2 27.4 - - + -
81A TYR* 4.7 9.0 - - + -
90A THR* 1.3 71.3 - - - +
92A TRP* 1.3 63.2 + - - +
93A VAL* 3.8 18.6 + - + -
103A SER* 4.4 0.3 + - - -
104A PRO* 2.9 27.9 - - - +
105A PHE* 3.1 51.2 + - + -
107A VAL* 3.4 17.3 - - + -
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Residues in contact with TRP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLN 2.9 14.8 - - - +
53A VAL* 3.2 2.4 - - - -
54A ALA* 2.7 43.1 + - + +
56A VAL* 5.0 12.3 - - + +
90A THR* 3.3 37.1 + - + +
91A VAL* 1.3 75.9 - - - +
93A VAL* 1.3 62.6 + - - +
94A CYS* 4.1 12.1 - - - -
104A PRO* 4.1 15.5 - - + +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.0 27.6 - - + -
32A PHE* 4.7 10.3 - - + -
34A LEU* 4.5 17.7 - - + -
51A VAL* 5.3 5.2 - - + -
52A GLN 3.3 4.9 - - - +
53A VAL* 4.8 7.4 - - + -
79A ILE* 5.3 1.1 - - + -
91A VAL* 3.8 22.0 - - + -
92A TRP* 1.3 77.5 - - - +
94A CYS* 1.3 68.2 + - - +
95A ILE* 5.6 0.2 - - + -
99A HIS* 4.2 0.2 - - - -
100A VAL* 3.5 23.1 + - + +
103A SER* 2.9 33.6 + - - +
104A PRO* 4.7 0.2 - - - +
105A PHE* 4.6 5.8 - - + -
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Residues in contact with CYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN 3.8 0.3 - - - +
51A VAL* 4.8 0.2 - - - +
52A GLN* 2.9 42.9 + - + +
92A TRP* 4.8 13.5 - - - -
93A VAL* 1.3 86.8 - - - +
95A ILE* 1.3 63.8 + - - +
97A GLU* 5.0 4.0 + - - -
98A GLN 3.1 24.9 - - - +
99A HIS* 3.7 20.4 - - - -
100A VAL* 4.4 1.6 - - - +
103A SER* 5.1 0.4 - - - -
104A PRO* 5.4 4.3 - - - -
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.7 9.2 - - + -
11A PRO* 4.0 14.0 - - + +
14A CYS* 3.8 23.8 - - + -
34A LEU* 4.0 22.4 - - + -
36A CYS* 5.2 5.6 - - - -
49A ASP* 4.4 11.2 - - + -
50A ASN 3.3 19.7 - - - +
51A VAL* 4.2 13.9 - - + -
93A VAL* 5.6 0.9 - - + -
94A CYS* 1.3 78.6 - - - +
96A LYS* 1.3 87.4 + - + +
97A GLU 3.2 1.1 - - - -
98A GLN* 2.8 26.1 + - - +
100A VAL* 3.8 20.1 - - + +
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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