Contacts of the strand formed by residues 162 - 167 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C HIS* 6.4 0.7 - - - -
115C CYS* 3.4 3.1 - - - +
116C ASN* 2.8 55.3 + - - +
117C TYR* 6.4 0.2 - - - -
160C ALA 4.2 3.7 + - - -
161C TYR* 1.3 73.9 - - - +
163C VAL* 1.3 59.8 - - - +
164C PHE* 4.1 17.9 - - - -
40D GLN* 3.5 23.0 + - - -
73D LEU* 4.0 9.4 - - - +
60G LEU* 5.1 1.8 - - - +
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Residues in contact with VAL 163 (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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94C HIS* 3.8 2.1 - - - +
95C PHE* 2.8 44.4 + - + +
113C PHE* 4.1 21.3 - - + -
114C ILE 3.8 2.7 - - - -
115C CYS* 3.8 24.2 - - + +
152C PHE* 4.5 6.3 - - + -
153C LEU* 4.4 11.2 - - + -
156C LEU* 3.2 32.3 - - + -
161C TYR* 3.2 5.9 + - + +
162C SER* 1.3 81.4 - - - +
164C PHE* 1.3 64.9 + - - +
60G LEU* 4.6 7.4 - - + -
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Residues in contact with PHE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 3.5 30.3 - - + -
92C ILE* 3.2 34.1 - - + -
93C ILE* 3.2 5.8 - - - +
94C HIS* 3.4 51.4 - + - -
95C PHE 4.8 0.2 - - - -
113C PHE* 3.2 11.5 - - - +
114C ILE 2.7 49.6 + - - +
115C CYS* 5.0 0.2 - - - -
121C TRP* 4.3 15.7 - + - -
162C SER* 4.1 20.6 - - - -
163C VAL* 1.3 75.0 - - - +
165C VAL* 1.3 60.4 + - - +
40D GLN* 4.7 0.7 - - - -
73D LEU* 3.8 24.2 - - + -
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLU 3.7 0.5 - - - +
92C ILE* 3.5 3.6 - - - -
93C ILE* 2.8 55.0 + - + +
94C HIS 5.0 1.3 - - - +
95C PHE* 4.5 3.9 - - + +
100C TYR* 4.0 30.1 - - + +
110C GLU* 3.6 39.5 - - + +
112C SER 4.0 4.0 - - - +
113C PHE* 3.8 18.4 - - + -
164C PHE* 1.3 74.6 - - - +
166C VAL* 1.3 64.1 + - - +
167C LYS* 3.9 10.2 + - + -
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Residues in contact with VAL 166 (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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23C LEU* 4.3 9.6 - - + -
85C LEU* 4.9 4.0 - - + -
90C LEU* 4.1 30.5 - - + -
91C GLU 3.3 9.9 - - - +
92C ILE* 4.6 6.5 - - + -
110C GLU* 4.8 3.1 - - - +
111C ARG* 5.6 2.8 + - - +
112C SER* 3.2 39.0 + - - +
114C ILE* 4.1 36.6 - - + +
164C PHE 4.5 0.2 - - - +
165C VAL* 1.3 78.3 - - - +
167C LYS* 1.3 67.7 + - - +
168C GLY 4.2 3.9 + - - +
170C LEU* 4.8 2.5 - - + -
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Residues in contact with LYS 167 (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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89C GLY 4.1 0.5 - - - +
90C LEU* 3.2 7.4 - - - +
91C GLU* 2.8 52.9 + - + +
93C ILE* 3.9 25.1 - - + -
100C TYR* 4.0 17.5 - - - -
103C LEU* 5.2 8.9 - - - +
105C ILE* 4.8 8.9 - - - +
110C GLU* 3.0 34.4 + - - +
165C VAL* 4.2 9.2 - - + -
166C VAL* 1.3 80.4 - - - +
168C GLY* 1.3 60.1 - - - +
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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