Contacts of the strand formed by residues 163 - 169 (chain C) in PDB entry 4QPL
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 163 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C TYR* 4.0 11.6 - - + -
108C GLU* 2.9 35.2 + - + +
109C GLY* 4.0 1.8 - - - -
152C VAL* 3.1 4.6 - - - +
153C GLN* 2.8 55.4 + - + +
161C ARG* 3.1 30.9 - - + +
162C ARG* 1.3 76.0 - - - +
164C LYS* 1.3 67.8 + - - +
165C ILE* 3.8 1.0 - - - +
201C V3L 2.6 98.3 + - - +
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Residues in contact with LYS 164 (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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107C TYR* 3.4 2.6 - - - -
108C GLU* 2.8 57.0 + - + +
113C TRP* 3.5 16.0 - - + -
151C MET 3.6 11.0 - - - +
152C VAL* 4.3 3.6 - - + +
162C ARG 4.0 1.1 + - - +
163C ARG* 1.3 73.8 - - - +
165C ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C TRP* 4.6 8.5 - - + -
106C TYR 3.2 11.9 - - - +
107C TYR* 4.2 1.3 - - + -
113C TRP* 4.1 5.0 - - - -
116C TYR* 3.1 30.5 - - + +
124C LEU* 5.0 2.0 - - + -
146C ALA* 4.5 9.4 - - + -
147C ASP 4.2 7.2 - - - +
148C LEU* 4.3 19.1 - - + -
151C MET* 3.0 42.6 + - + +
152C VAL 3.8 20.2 - - - +
153C GLN* 3.9 10.1 - - + +
163C ARG 3.8 9.2 - - - +
164C LYS* 1.3 80.5 - - - +
166C LYS* 1.3 65.6 + - - +
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Residues in contact with LYS 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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104C ALA 3.9 0.3 - - - +
105C TRP* 3.4 10.0 - - - -
106C TYR* 2.9 40.1 + - + +
113C TRP* 3.4 51.7 - - + +
151C MET* 3.8 8.3 - - - -
165C ILE* 1.3 77.2 - - - +
167C ARG* 1.3 62.9 + - - +
168C ASP* 3.0 38.0 + - + +
172C ILE* 3.8 22.1 - - - +
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Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 3.5 42.1 - - + +
104C ALA 3.4 9.9 - - - +
105C TRP* 3.7 35.2 - - + +
125C GLU* 2.8 37.1 + - - -
128C PHE* 4.3 20.0 - - + -
151C MET* 4.3 5.0 - - + +
166C LYS* 1.3 74.9 - - - +
168C ASP* 1.3 62.9 + - - +
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Residues in contact with ASP 168 (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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103C TYR* 3.3 6.7 - - - -
104C ALA 2.8 32.2 + - - +
106C TYR* 3.8 8.1 - - + -
166C LYS* 3.0 41.7 + - + +
167C ARG* 1.3 75.6 - - - +
169C ILE* 1.3 91.6 + - - +
172C ILE* 4.6 9.2 - - + +
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Residues in contact with ILE 169 (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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102C GLU* 3.2 15.5 - - + +
103C TYR* 4.1 0.9 - - + +
106C TYR* 2.8 18.5 + - - -
168C ASP* 1.3 98.2 + - - +
170C ILE* 1.3 61.1 + - - +
171C ASP* 3.8 28.7 - - + +
172C ILE* 3.8 18.2 - - + +
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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
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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