Contacts of the strand formed by residues 94 - 102 (chain C) in PDB entry 2H8C
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 94 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C VAL* 3.3 25.4 - - + +
57C ILE* 4.5 2.9 - - + -
79C PHE* 3.9 19.5 - - + -
88C TRP* 3.8 22.9 - - + -
91C ASP* 2.5 35.3 + - + +
92C ALA* 3.9 7.4 - - - +
93C GLN* 1.3 67.3 - - - +
95C VAL* 1.3 60.9 + - - +
96C ASP 3.9 8.5 - - - +
97C TYR* 3.7 34.1 - - + -
71D LEU* 3.9 14.6 - - + +
101D LYS* 4.9 2.9 - - - -
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Residues in contact with VAL 95 (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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54C PRO* 3.5 32.5 - - + -
55C VAL 3.2 10.9 + - - +
92C ALA 5.6 0.7 - - - +
93C GLN 3.0 2.4 + - - +
94C VAL* 1.3 74.0 - - - +
96C ASP* 1.3 60.1 + - + +
117C MET* 4.5 10.1 - - + -
71D LEU* 4.5 3.4 - - - -
100D VAL* 3.7 2.1 - - - +
101D LYS* 2.7 74.7 + - + +
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Residues in contact with ASP 96 (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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55C VAL 3.9 1.3 + - - +
56C LYS* 3.2 29.1 - - + +
57C ILE* 2.6 34.3 + - - +
94C VAL* 3.3 4.6 - - - +
95C VAL* 1.3 85.9 - - + +
97C TYR* 1.3 58.0 + - - +
71D LEU* 4.9 0.4 - - - +
98D ARG* 3.4 40.4 + - - +
99D VAL 3.7 4.9 - - - -
100D VAL* 3.6 18.8 - - + +
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Residues in contact with TYR 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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57C ILE* 3.2 22.9 - - + -
59C ILE* 4.8 0.4 - - + -
75C GLN* 3.3 28.7 + - + -
79C PHE* 3.7 17.0 - + + -
94C VAL* 3.7 13.5 - - + -
96C ASP* 1.3 75.1 + - - +
98C ARG* 1.3 57.7 + - - +
99C VAL* 3.6 22.2 - - + -
71D LEU* 4.1 16.6 - - + -
72D ASP* 3.4 26.2 + - - +
75D GLN* 3.7 12.6 + - - +
97D TYR* 3.7 11.7 - + - +
98D ARG* 3.1 4.6 - - - -
99D VAL* 2.8 71.6 + - + +
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Residues in contact with ARG 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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57C ILE 2.7 13.6 + - - +
58C ARG* 3.0 24.3 - - + +
59C ILE* 2.6 33.8 + - - +
97C TYR* 1.3 73.6 - - - +
99C VAL* 1.3 57.5 + - - +
100C VAL* 3.9 7.9 - - + -
56D LYS* 4.0 21.3 - - - +
96D ASP* 2.7 39.6 + - - +
97D TYR 3.3 3.8 - - - -
98D ARG* 3.4 52.4 - - - +
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Residues in contact with VAL 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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59C ILE* 3.6 22.0 - - + +
61C CYS* 3.9 22.7 - - - -
71C LEU* 3.9 29.2 - - + +
75C GLN* 3.9 8.7 - - + +
97C TYR* 3.6 31.6 - - + -
98C ARG* 1.3 76.5 - - - +
100C VAL* 1.3 63.0 + - - +
95D VAL 3.7 1.6 - - - +
96D ASP* 3.3 3.1 - - - -
97D TYR* 2.7 49.5 + - + +
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Residues in contact with VAL 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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58C ARG* 3.9 25.4 - - + +
59C ILE 2.9 13.5 + - - +
60C GLU* 3.7 3.8 - - - -
61C CYS* 2.6 38.4 + - - +
98C ARG* 3.9 15.0 - - + +
99C VAL* 1.3 78.7 - - - +
101C LYS* 1.3 72.8 + - - +
102C MET* 3.1 12.6 + - + -
95D VAL 3.3 10.1 - - - +
96D ASP* 3.2 28.9 - - + +
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Residues in contact with LYS 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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61C CYS* 3.7 6.7 - - - -
63C MET* 3.8 34.5 - - + -
71C LEU* 4.3 12.0 - - + +
100C VAL* 1.3 76.9 - - - +
102C MET* 1.3 64.0 + - - +
95D VAL* 2.8 40.4 + - + +
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Residues in contact with MET 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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58C ARG* 5.0 2.0 - - - -
60C GLU* 3.7 38.4 - - + +
61C CYS 2.6 19.9 + - - +
62C HIS* 3.4 37.5 - - + +
63C MET* 3.3 14.4 + - - +
100C VAL* 3.1 13.1 + - - +
101C LYS* 1.3 82.6 - - - +
103C PRO* 1.3 89.4 - - + +
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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