Contacts of the strand formed by residues 145 - 148 (chain Q) in PDB entry 5C3I
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 145 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Q ARG 3.4 6.1 - - - +
110Q GLY* 2.9 35.1 + - - +
112Q TYR* 4.3 2.2 - - + -
143Q ASN* 3.5 23.1 + - - +
144Q PRO* 1.3 83.6 + - - +
146Q VAL* 1.3 61.9 + - - +
147Q THR 3.7 0.3 + - - -
105R GLU* 4.4 6.3 - - - +
106R ASP* 2.6 46.2 + - - +
109R LEU* 3.4 22.7 - - - +
130R ILE* 3.7 41.6 - - + +
131R ARG* 4.3 1.0 - - + +
96S THR* 4.4 12.8 - - + -
97S LEU 4.1 3.1 - - - -
98S TYR* 3.2 40.5 - - - +
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Residues in contact with VAL 146 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q ILE* 3.7 28.7 - - + -
108Q ARG 4.0 2.7 - - - -
109Q VAL* 4.4 6.1 - - + +
144Q PRO* 4.7 3.4 - - + -
145Q ARG* 1.3 72.3 - - - +
147Q THR* 1.3 60.8 + - - +
148Q ARG* 4.2 13.4 + - + +
95S ARG 3.6 2.1 - - - +
96S THR* 3.2 1.7 - - - -
97S LEU* 3.0 38.4 + - + +
99S GLY* 3.4 33.2 - - - +
100S PHE* 3.5 37.7 - - + -
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Residues in contact with THR 147 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q ILE* 3.4 3.2 - - - +
108Q ARG* 2.8 43.1 + - - -
145Q ARG 4.2 0.9 + - - -
146Q VAL* 1.3 73.2 - - - +
148Q ARG* 1.3 63.6 + - - +
149Q PHE* 3.7 22.9 - - + -
130R ILE 3.7 5.4 + - - -
131R ARG* 3.3 36.7 - - - +
93S GLN 5.2 0.2 - - - +
94S GLY 4.4 6.3 - - - +
95S ARG 3.3 8.7 - - - +
96S THR* 2.8 29.9 + - - +
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Residues in contact with ARG 148 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q ALA* 4.5 11.5 - - - +
4Q VAL 5.0 0.8 + - - -
5Q GLN* 3.2 45.6 - - - +
6Q VAL 6.0 0.8 - - - +
106Q PHE 3.5 7.6 + - - +
107Q ILE* 4.2 21.3 - - + +
146Q VAL* 4.3 12.6 - - + +
147Q THR* 1.3 77.0 - - - +
149Q PHE* 1.3 63.7 + - - +
91S LYS 4.4 2.1 - - - +
94S GLY* 3.2 4.7 - - - -
95S ARG* 2.9 52.8 + - + +
97S LEU* 6.1 8.5 - - - -
101S GLY 5.2 7.5 + - - -
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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