Contacts of the strand formed by residues 162 - 167 (chain E) in PDB entry 3O65
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 SER 162 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E HIS* 4.1 7.7 - - - -
115E CYS* 3.6 2.8 - - - +
116E ASN* 3.0 33.2 + - - +
156E LEU* 5.5 0.5 - - - +
157E GLN* 4.5 1.3 - - - -
160E ALA 3.5 4.9 + - - -
161E TYR* 1.3 75.9 - - - +
163E VAL* 1.3 64.1 + - - +
164E PHE* 3.4 32.2 - - - -
37F PRO* 4.5 4.0 - - - +
40F GLN* 2.8 26.3 + - - -
73F LEU* 4.2 7.5 - - - +
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Residues in contact with VAL 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E HIS* 3.9 0.9 - - - -
95E PHE* 2.9 45.5 + - + +
113E PHE* 4.3 10.3 - - + -
114E ILE 3.9 2.5 - - - -
115E CYS* 4.2 8.5 - - - +
153E LEU* 3.8 28.5 - - + +
156E LEU* 3.8 34.1 - - + -
157E GLN* 3.7 26.5 + - + +
162E SER* 1.3 79.7 - - - +
164E PHE* 1.3 66.0 + - - +
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Residues in contact with PHE 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ILE* 3.3 27.1 - - + -
92E ILE* 3.1 40.2 - - + -
93E ILE 3.8 2.7 - - - +
94E HIS* 3.2 54.3 - + - -
113E PHE* 3.2 10.2 - - - +
114E ILE* 2.7 51.2 + - + +
115E CYS* 4.9 0.4 - - - -
116E ASN* 5.0 0.4 - - + -
121E TRP* 4.1 19.1 - + - -
162E SER* 3.4 32.1 - - - -
163E VAL* 1.3 74.7 - - - +
165E VAL* 1.3 59.8 + - - +
73F LEU* 4.1 5.6 - - + -
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Residues in contact with VAL 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E GLU 3.6 2.4 - - - +
92E ILE* 3.7 1.4 - - - -
93E ILE* 3.1 53.1 + - + +
95E PHE* 4.6 4.9 - - + +
100E TYR* 4.1 23.3 - - + +
110E GLU* 3.3 42.4 - - + +
112E SER 4.3 2.0 - - - +
113E PHE* 3.7 18.3 - - + -
163E VAL 4.3 0.2 - - - -
164E PHE* 1.3 72.4 - - - +
166E VAL* 1.3 65.4 + - - +
167E LYS* 3.7 11.1 + - + -
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Residues in contact with VAL 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 4.4 17.5 - - + -
85E LEU* 4.7 7.6 - - + -
90E LEU* 4.4 22.2 - - + -
91E GLU 3.4 11.2 - - - +
92E ILE* 5.2 2.5 - - + -
110E GLU* 4.4 5.2 - - - +
111E ARG* 5.4 2.6 + - - +
112E SER* 3.2 38.6 + - - +
113E PHE 4.1 1.3 - - - -
114E ILE* 3.8 42.4 - - + +
164E PHE 4.1 1.1 - - - +
165E VAL* 1.3 79.5 - - - +
167E LYS* 1.3 63.2 + - - +
168E GLY 4.1 3.9 + - - +
170E LEU* 5.0 1.3 - - + -
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Residues in contact with LYS 167 (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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89E GLY 4.3 0.3 - - - +
90E LEU* 3.4 5.2 - - - +
91E GLU* 2.8 47.1 + - + +
93E ILE* 3.9 27.6 - - + -
100E TYR* 3.7 19.1 - - - -
103E LEU* 5.3 3.0 - - - +
105E ILE* 3.7 16.8 - - - +
110E GLU* 3.2 37.4 + - - +
165E VAL* 3.7 7.6 + - + -
166E VAL* 1.3 73.2 - - - +
168E GLY* 1.3 59.2 + - - +
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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
------------------------------------------------------------
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