Contacts of the strand formed by residues 159 - 164 (chain V) in PDB entry 5MQF
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 ILE 159 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17V GLU 3.6 9.4 - - - +
18V THR* 3.8 8.3 - - - -
48V TYR* 3.6 18.8 - - + +
49V ASN* 3.8 0.8 - - - -
50V GLY* 2.7 32.7 + - - -
51V THR 2.5 19.0 + - - +
157V VAL 3.9 0.2 + - - -
158V LYS* 1.3 71.4 - - - +
160V ILE* 1.3 61.5 + - - +
161V LYS 4.8 4.3 - - - +
162V ALA* 6.3 1.6 - - + -
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Residues in contact with ILE 160 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V GLU* 2.6 23.7 + - + +
18V THR* 3.4 13.9 - - - +
19V SER 5.0 0.2 - - - +
49V ASN* 4.3 8.5 - - - +
50V GLY* 4.4 1.6 + - - -
158V LYS 3.4 1.7 + - - +
159V ILE* 1.3 75.6 - - - +
161V LYS* 1.3 62.6 + - + +
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Residues in contact with LYS 161 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V TYR 3.8 0.6 - - - +
17V GLU* 2.9 39.6 + - + +
49V ASN* 4.5 11.4 - - + +
159V ILE* 3.5 3.2 - - - +
160V ILE* 1.3 82.2 - - + +
162V ALA* 1.3 63.0 - - - +
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Residues in contact with ALA 162 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL* 6.0 3.1 - - + -
15V TYR 3.2 8.3 - - - +
16V LEU* 5.2 2.7 - - - -
43V ALA* 3.8 30.9 - - + +
48V TYR* 5.1 11.9 - - + -
49V ASN* 4.9 8.9 - - + +
161V LYS* 1.3 77.9 - - - +
163V TYR* 1.3 60.9 + - - +
164V PRO* 3.3 11.9 - - - +
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Residues in contact with TYR 163 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL* 3.1 3.5 - - - -
15V TYR* 2.9 47.8 + - + +
43V ALA* 5.7 0.2 - - - -
162V ALA* 1.3 71.6 - - - +
164V PRO* 1.4 62.9 - - - +
165V SER* 2.8 14.5 + - - +
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Residues in contact with PRO 164 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V PRO* 4.9 5.3 - - + +
13V ASN 3.4 7.4 - - - +
14V VAL* 4.5 4.3 - - + -
40V ALA* 4.5 15.7 - - + +
43V ALA* 4.5 8.5 - - + +
44V ARG* 3.7 37.5 - - + +
162V ALA 3.3 11.2 - - - +
163V TYR* 1.4 76.8 - - - +
165V SER* 1.3 66.9 + - - +
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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