Contacts of the strand formed by residues 95 - 99 (chain E) in PDB entry 1H4O
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 ARG 95 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLU* 2.4 48.7 + - - +
23E VAL* 4.3 11.3 - - - +
28E LEU* 3.0 32.5 - - + +
69E VAL* 4.8 11.7 - - + +
70E VAL 2.9 19.1 + - - +
71E ALA* 3.3 11.8 - - + +
72E CYS 2.9 26.5 + - - +
94E VAL* 1.3 74.2 - - - +
96E LEU* 1.3 60.1 + - - +
97E LEU* 3.7 8.6 + - + +
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLU* 3.4 30.6 + - + +
17E GLY 4.4 2.3 + - - -
52E LEU* 4.3 7.4 - - + -
72E CYS* 3.7 17.5 - - + +
74E SER* 6.1 0.4 - - - +
81E THR* 3.7 32.4 + - + +
82E GLY* 5.0 2.9 - - - +
84E TRP* 3.6 35.7 - - + -
85E GLY* 3.7 11.7 - - - -
90E ALA* 3.6 21.1 - - + -
94E VAL* 3.5 22.2 + - + +
95E ARG* 1.3 73.2 - - - +
97E LEU* 1.3 61.6 + - - +
98E ALA 4.3 0.2 + - - -
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Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E VAL* 4.0 11.2 - - + -
15E PHE 3.3 3.6 - - - +
16E GLU* 4.0 26.2 - - + +
23E VAL* 4.4 13.7 - - + -
25E LEU* 4.0 17.0 - - + -
28E LEU* 3.8 16.6 - - + -
36E LEU* 4.9 1.8 - - + -
71E ALA* 3.4 29.8 - - + -
72E CYS 2.7 17.0 + - - +
73E LEU* 3.4 17.1 - - + +
74E SER* 3.1 27.9 + - - -
81E THR* 4.3 3.4 - - - +
95E ARG* 4.2 8.1 - - + +
96E LEU* 1.3 83.2 - - - +
98E ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E VAL* 3.3 6.7 - - - +
15E PHE* 2.7 36.0 + - + +
74E SER 3.7 4.0 - - - -
76E ASN 3.3 18.2 - - - +
77E ASP 3.7 0.7 - - - -
78E ALA* 3.5 21.1 - - + +
81E THR* 3.5 23.1 + - + +
97E LEU* 1.3 73.7 - - - +
99E ASP* 1.3 57.9 + - - +
100E PRO* 3.4 10.4 - - + +
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Residues in contact with ASP 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E VAL* 4.8 0.3 - - - +
13E GLU 4.8 2.8 - - - +
14E VAL* 4.0 14.1 - - + +
73E LEU* 3.9 18.1 - - + +
74E SER 2.9 15.9 + - - +
75E VAL* 3.3 17.0 - - + +
76E ASN 3.7 0.2 + - - -
97E LEU 4.1 0.2 + - - -
98E ALA* 1.3 71.7 - - - +
100E PRO* 1.3 68.6 - - - +
101E THR* 4.1 2.8 + - - -
102E GLY* 3.0 15.1 + - - -
103E ALA* 3.0 28.6 + - - +
104E PHE* 2.7 36.4 + - - +
105E GLY 4.1 0.7 + - - -
125E LEU* 5.4 1.8 - - + +
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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