Contacts of the strand formed by residues 94 - 102 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LEU* 3.6 14.9 - - + +
55D VAL* 3.6 14.4 - - + -
57D ILE* 2.7 39.7 - - + -
79D PHE* 4.2 10.5 - - + -
88D TRP* 3.6 28.3 - - + -
91D ASP 3.6 14.8 - - - +
92D ALA 3.0 10.6 + - - +
93D GLN* 1.3 75.2 - - - +
95D VAL* 1.3 63.2 + - - +
96D ASP 4.1 2.7 - - - +
97D TYR* 4.0 23.1 - - + -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 4.1 4.4 - - - +
99C VAL 3.7 1.5 - - - +
100C VAL* 3.3 5.2 - - - +
101C LYS* 2.8 52.8 + - + +
54D PRO* 4.3 9.9 - - + -
55D VAL 3.3 14.4 + - - +
92D ALA 4.9 2.5 - - - +
93D GLN 3.7 10.1 - - - +
94D VAL* 1.3 77.5 - - - +
96D ASP* 1.3 63.7 + - + +
117D MET* 3.3 34.3 - - + -
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Residues in contact with ASP 96 (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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58C ARG* 4.7 0.9 + - - -
98C ARG* 2.7 39.7 + - - -
99C VAL 3.3 4.5 - - - -
100C VAL* 3.2 26.5 - - + +
55D VAL 3.6 0.6 + - - -
56D LYS* 3.1 32.0 - - + +
57D ILE* 3.0 24.3 + - - +
94D VAL* 4.3 1.6 - - - -
95D VAL* 1.3 86.9 - - + +
97D TYR* 1.3 65.0 + - - +
98D ARG 4.1 0.5 + - - -
117D MET* 5.5 4.0 - - + -
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Residues in contact with TYR 97 (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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71C LEU* 3.9 22.5 - - + -
72C ASP* 3.2 30.5 + - - -
75C GLN* 4.0 9.2 - - - +
97C TYR* 3.7 19.2 - + - +
98C ARG* 3.3 1.2 - - - -
99C VAL* 2.7 59.5 + - + -
57D ILE* 3.0 29.2 - - + +
59D ILE* 5.6 0.9 - - + -
75D GLN* 3.3 39.3 + - + -
79D PHE* 3.8 12.8 - + + -
94D VAL* 4.0 14.6 - - + -
96D ASP* 1.3 75.6 + - - +
98D ARG* 1.3 57.5 + - - +
99D VAL* 4.3 11.0 - - + -
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Residues in contact with ARG 98 (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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96C ASP* 3.4 38.0 + - - +
97C TYR 3.1 11.7 - - - +
98C ARG* 3.4 50.6 - - + +
57D ILE 3.1 7.0 + - - +
58D ARG* 3.2 34.6 - - + +
59D ILE* 2.7 30.5 + - - +
96D ASP* 4.1 0.8 + - - -
97D TYR* 1.3 73.5 - - - +
99D VAL* 1.3 55.9 + - - +
100D VAL* 3.6 14.7 - - + +
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Residues in contact with VAL 99 (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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95C VAL 4.4 0.2 - - - +
96C ASP* 3.7 1.0 - - - -
97C TYR* 2.8 51.6 + - + +
59D ILE* 3.3 26.5 - - + -
61D CYS* 3.9 18.4 - - - -
71D LEU* 3.7 30.0 - - + +
75D GLN* 3.6 33.4 - - + +
97D TYR* 4.0 6.0 + - + -
98D ARG* 1.3 71.3 - - - +
100D VAL* 1.3 67.3 + - - +
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Residues in contact with VAL 100 (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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95C VAL 3.7 7.0 - - - +
96C ASP* 3.5 29.6 - - + +
58D ARG* 4.0 29.4 - - + +
59D ILE 2.5 12.8 + - - +
60D GLU* 3.2 5.7 - - - -
61D CYS* 2.7 31.8 + - - -
98D ARG* 3.6 21.5 - - + +
99D VAL* 1.3 85.4 - - - +
101D LYS* 1.3 66.3 + - - +
102D MET* 4.6 9.6 - - + -
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Residues in contact with LYS 101 (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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92C ALA 5.0 7.6 - - - -
94C VAL 4.9 4.5 - - - -
95C VAL* 2.7 54.9 + - + +
61D CYS* 3.7 7.2 - - - -
63D MET* 3.8 37.2 - - + +
71D LEU* 4.1 16.8 - - + +
100D VAL* 1.3 75.3 - - - +
102D MET* 1.3 72.0 + - - +
103D PRO* 4.0 3.8 - - - +
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Residues in contact with MET 102 (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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58D ARG* 5.3 2.7 - - - -
60D GLU* 3.4 38.4 - - + +
61D CYS 2.4 35.5 + - - +
62D HIS* 3.6 28.3 - - + +
63D MET* 3.4 15.6 + - - +
100D VAL* 3.5 11.4 + - + +
101D LYS* 1.3 78.2 - - - +
103D PRO* 1.3 91.1 - - + +
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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