Contacts of the strand formed by residues 1290 - 1295 (chain N) in PDB entry 4G7H
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 LEU1290 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1284N GLU* 3.3 5.6 - - - +
1285N GLU* 3.3 28.5 - - + +
1286N THR 3.4 19.5 - - - +
1288N GLU 6.0 0.2 - - - -
1289N LYS* 1.3 87.3 - - - +
1291N SER* 1.3 63.5 + - - +
1304N LYS* 4.7 1.4 - - - +
1305N LEU* 3.0 30.8 + - + +
1306N PRO 5.1 1.8 - - - +
1307N LYS* 3.9 44.9 - - + +
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Residues in contact with SER1291 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283N ILE* 3.7 3.1 - - - +
1284N GLU* 2.9 57.8 + - - +
1285N GLU* 5.1 0.5 - - - +
1290N LEU* 1.3 75.0 - - - +
1292N VAL* 1.3 75.9 + - - +
1293N PHE* 3.6 16.0 - - - -
1302N GLU* 4.1 8.0 + - - +
1303N TYR 3.2 16.0 + - - -
1304N LYS* 4.0 7.9 - - - +
1305N LEU* 4.7 2.9 - - - +
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Residues in contact with VAL1292 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281N VAL* 4.8 11.4 - - + -
1282N ARG 3.8 9.6 - - - +
1283N ILE* 5.8 4.3 - - + -
1291N SER* 1.3 84.4 + - - +
1293N PHE* 1.3 73.5 + - - +
1294N VAL* 4.2 5.1 + - + -
1301N LYS 3.9 0.3 - - - +
1303N TYR* 2.9 44.0 + - + +
1305N LEU* 4.0 26.0 - - + -
1311N LEU* 4.2 19.3 - - + -
1313N VAL* 5.8 2.2 - - + -
1325N LEU* 4.7 21.5 - - + -
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Residues in contact with PHE1293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1280N VAL 3.5 2.6 - - - +
1281N VAL* 3.8 1.2 - - - -
1282N ARG* 2.9 71.9 + - + +
1284N GLU* 4.4 13.9 - - + -
1291N SER* 3.6 22.2 - - - -
1292N VAL* 1.3 80.3 - - - +
1294N VAL* 1.3 62.6 + - - +
1295N GLU* 3.7 27.3 + - + +
1300N SER* 5.5 3.8 - - - -
1301N LYS 3.4 7.2 - - - +
1302N GLU* 3.5 45.8 - - + -
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Residues in contact with VAL1294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275N SER* 4.1 10.1 - - - -
1277N ILE* 3.9 27.8 - - + +
1278N ASP 4.0 2.7 - - - +
1279N GLY* 3.9 19.3 - - - -
1280N VAL 3.4 5.2 - - - +
1281N VAL* 5.5 4.5 - - + -
1292N VAL* 4.2 5.1 - - + -
1293N PHE* 1.3 72.5 - - - +
1295N GLU* 1.3 61.2 + - - +
1296N SER 4.2 0.3 + - - -
1299N PHE 4.4 0.3 - - - +
1300N SER* 3.6 1.4 - - - -
1301N LYS* 2.9 37.1 + - + +
1303N TYR* 3.9 26.7 - - + -
1319N VAL* 4.0 16.4 - - + -
1325N LEU* 4.2 13.2 - - + -
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Residues in contact with GLU1295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278N ASP 5.1 0.2 - - - -
1279N GLY* 3.7 1.5 - - - -
1280N VAL* 2.9 55.9 + - + +
1282N ARG* 2.3 55.7 + - - +
1293N PHE* 3.7 20.5 - - + +
1294N VAL* 1.3 77.5 - - - +
1296N SER* 1.3 62.6 + - - +
1299N PHE 3.9 2.2 - - - -
1300N SER* 3.6 22.4 - - - -
1301N LYS 4.9 0.2 - - - +
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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