Contacts of the strand formed by residues 96 - 102 (chain C) in PDB entry 2P5V
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 VAL 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C VAL* 3.7 23.6 - - + -
93C TRP* 3.0 27.3 + - + +
94C PRO 4.2 2.2 - - - +
95C GLU* 1.3 77.8 - - + +
97C LEU* 1.3 59.8 + - - +
98C SER 3.5 23.1 - - - +
110C LEU* 3.9 16.6 - - + -
111C GLN 3.7 6.1 - - - +
112C ALA* 4.0 7.4 - - + -
123C PHE* 3.8 29.8 - - + -
147D LYS* 2.6 34.2 + - + +
149D THR* 4.6 0.9 - - - +
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PRO 4.0 1.3 - - - +
95C GLU 3.5 17.5 - - - +
96C VAL* 1.3 77.4 - - - +
98C SER* 1.3 61.9 + - - +
111C GLN* 2.8 18.5 + - + +
113C PHE* 3.9 26.7 - - + -
147D LYS* 4.0 2.7 - - - +
148D HIS* 3.4 3.3 + - - -
149D THR* 2.8 50.8 + - - +
150D THR* 4.0 9.6 - - - +
151D SER 3.3 27.1 - - - +
152D LEU* 3.8 20.0 - - + -
153D PRO* 4.0 13.7 - - + -
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C VAL* 3.5 7.6 - - - +
97C LEU* 1.3 82.7 - - - +
99C CYS* 1.3 62.1 + - - +
100C PHE* 3.7 22.2 - - - -
109C LEU 4.2 1.3 - - - -
110C LEU* 3.3 4.2 - - - -
111C GLN* 3.0 49.1 + - - +
111D GLN* 5.7 0.3 + - - -
147D LYS* 3.1 13.5 - - - -
148D HIS* 3.8 15.5 - - - -
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Residues in contact with CYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C PHE* 4.0 10.5 - - - -
90C VAL* 3.7 21.5 - - + -
98C SER* 1.3 77.0 - - - +
100C PHE* 1.3 63.7 + - - +
108C TYR* 3.8 18.4 - - - -
109C LEU 3.2 5.2 - - - -
110C LEU* 3.4 25.4 - - + -
146D ILE* 2.8 47.2 + - + -
147D LYS* 2.8 14.9 + - + +
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Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C SER* 3.7 24.2 - - - -
99C CYS* 1.3 76.8 - - - +
101C ALA* 1.3 61.7 + - - +
102C LEU* 3.5 20.3 + - + +
108C TYR* 3.2 7.2 - - - -
109C LEU* 2.9 38.6 + - + +
69D GLN* 3.6 24.2 - - - -
71D PHE* 3.6 26.0 - + + -
111D GLN* 4.4 5.6 - - - -
142D VAL* 3.7 17.0 - - + -
144D LYS 3.5 2.2 - - - +
145D GLU* 3.6 42.4 - - + -
147D LYS 4.4 0.2 - - - -
148D HIS* 4.0 23.1 - + + -
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 5.1 0.9 - - + -
83C ARG* 4.3 5.8 - - - +
100C PHE* 1.3 72.3 - - - +
102C LEU* 1.3 54.7 + - - +
107C ASP 3.2 12.1 - - - +
108C TYR* 3.9 20.7 - - + -
1016C CL 4.1 9.4 - - + -
142D VAL* 3.6 5.0 - - - -
143D LEU* 2.7 39.8 + - + -
144D LYS* 2.9 30.6 + - + +
146D ILE* 4.3 0.8 - - - +
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C PHE* 3.7 28.5 - - + +
101C ALA* 1.3 80.2 - - - +
103C THR* 1.3 63.2 + - - +
104C GLY 3.5 4.1 + - - +
106C THR* 3.6 28.1 - - - +
107C ASP* 3.1 11.2 + - - +
109C LEU* 3.9 26.0 - - + +
71D PHE* 3.8 27.4 - - + -
73D ARG* 6.0 0.9 - - - +
140D SER* 3.2 24.0 - - - +
141D PHE 3.2 12.6 - - - +
142D VAL* 3.9 4.5 - - + -
143D LEU* 3.2 17.8 - - - +
903D GOL 5.5 4.0 - - - +
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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