Contacts of the strand formed by residues 55 - 62 (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 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D LEU* 4.5 18.2 - - + -
53D MET* 3.8 8.7 - - - +
54D PRO* 1.3 81.6 - - - +
56D LYS* 1.3 59.0 + - - +
57D ILE 4.2 0.4 + - - -
88D TRP* 4.4 10.5 - - + -
93D GLN* 3.4 32.7 + - + +
94D VAL* 3.6 19.3 - - + -
95D VAL* 3.3 30.6 + - - +
96D ASP 3.6 2.4 + - - +
114D ILE* 4.0 22.7 - - + -
115D THR 3.7 4.3 - - - -
116D GLU* 4.4 11.4 - - + +
117D MET* 4.6 2.5 - - - -
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Residues in contact with LYS 56 (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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98C ARG* 4.0 20.0 - - - +
55D VAL* 1.3 74.9 - - - +
57D ILE* 1.3 66.4 + - - +
58D ARG* 5.1 1.1 - - + +
96D ASP* 3.1 37.9 - - + +
113D THR 3.1 2.7 - - - +
114D ILE* 3.0 7.3 - - - -
115D THR* 3.0 55.0 + - - +
117D MET* 4.5 16.5 - - - +
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Residues in contact with ILE 57 (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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55D VAL* 4.6 1.1 - - + +
56D LYS* 1.3 79.2 - - - +
58D ARG* 1.3 68.3 + - - +
59D ILE* 4.6 3.6 - - + -
79D PHE* 3.6 13.9 - - + -
82D LEU* 5.3 3.1 - - + -
88D TRP* 4.1 15.3 - - + -
94D VAL* 2.7 53.2 - - + -
96D ASP 3.0 5.5 + - - +
97D TYR* 3.0 44.0 - - + +
98D ARG 3.1 4.9 + - - +
112D LEU* 4.4 15.7 - - + -
113D THR 3.1 1.6 - - - +
114D ILE* 3.7 27.8 - - + -
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Residues in contact with ARG 58 (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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56D LYS* 5.1 1.2 - - + +
57D ILE* 1.3 73.8 - - - +
59D ILE* 1.3 63.6 + - - +
60D GLU* 2.7 45.0 + - + +
98D ARG* 3.2 43.8 - - + +
100D VAL* 4.0 22.5 - - + +
102D MET* 5.3 2.8 - - - -
111D GLU 4.6 0.2 - - - +
112D LEU* 3.3 9.0 - - - +
113D THR* 2.9 52.1 + - - +
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Residues in contact with ILE 59 (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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57D ILE* 4.6 6.7 - - + +
58D ARG* 1.3 74.3 - - - +
60D GLU* 1.3 65.9 + - - +
61D CYS* 3.7 7.7 + - - -
75D GLN* 4.0 17.3 - - + +
78D ALA* 4.1 9.0 - - + -
79D PHE* 3.8 27.6 - - + -
97D TYR* 5.8 0.7 - - + -
98D ARG 2.7 12.4 + - - +
99D VAL* 3.3 23.9 - - + +
100D VAL* 2.5 35.1 + - - +
110D LEU* 4.2 20.6 - - + -
111D GLU 3.8 2.2 - - - +
112D LEU* 3.4 28.0 - - + -
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Residues in contact with GLU 60 (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* 2.7 46.5 + - + +
59D ILE* 1.3 73.8 - - - +
61D CYS* 1.3 61.3 + - - +
62D HIS* 3.5 17.7 + - + -
100D VAL* 3.2 6.5 - - + -
102D MET* 3.4 31.8 - - + +
109D ARG 3.5 1.9 - - - +
110D LEU* 3.3 7.4 - - - -
111D GLU* 3.1 46.1 + - + +
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Residues in contact with CYS 61 (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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10D TRP* 4.6 0.4 - - + -
59D ILE* 4.2 7.2 - - - -
60D GLU* 1.3 74.1 - - - +
62D HIS* 1.3 60.2 + - - +
63D MET* 3.5 14.1 + - - +
71D LEU* 3.9 9.4 - - + -
74D LEU* 3.3 37.9 - - + -
99D VAL* 3.9 27.8 - - - -
100D VAL 2.7 11.8 + - - +
101D LYS* 3.5 1.5 - - - -
102D MET 2.4 32.9 + - - +
109D ARG 3.6 3.1 - - - -
110D LEU* 4.0 9.9 - - - -
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Residues in contact with HIS 62 (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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10D TRP* 3.4 3.4 - - - -
60D GLU* 3.5 24.8 + - + -
61D CYS* 1.3 70.1 - - - +
63D MET* 1.3 70.1 + - - +
102D MET* 3.4 32.5 - - + +
103D PRO* 3.7 11.0 - - + +
105D THR* 3.6 21.5 - - + -
108D GLY* 2.9 2.6 - - - -
109D ARG* 2.6 55.4 + - + +
111D GLU* 3.2 29.9 + - - -
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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