Contacts of the strand formed by residues 1279 - 1285 (chain N) in PDB entry 5X22
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 GLY1279 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1278N ASP* 1.3 79.9 - - - +
1280N VAL* 1.3 60.9 + - - -
1294N VAL* 3.9 8.6 - - - +
1295N GLU 3.5 12.3 - - - -
1296N SER* 4.1 5.4 - - - -
1317N ASP 3.4 0.9 - - - +
1318N TYR* 3.4 36.6 - - - -
1319N VAL* 3.5 7.9 + - - +
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Residues in contact with VAL1280 (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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1279N GLY* 1.3 74.8 - - - -
1281N VAL* 1.3 69.3 + - - +
1282N ARG* 3.6 2.6 + - + -
1293N PHE 3.5 0.3 - - - +
1294N VAL* 3.3 6.2 - - - -
1295N GLU* 2.9 57.4 + - + +
1316N GLY* 3.9 22.0 - - - -
1317N ASP 3.2 9.6 - - - +
1318N TYR* 4.9 0.9 - - + +
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Residues in contact with VAL1281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1280N VAL* 1.3 77.7 - - - +
1282N ARG* 1.3 60.9 + - - +
1283N ILE* 4.2 19.7 - - + -
1292N VAL* 4.3 11.9 - - + -
1293N PHE 3.7 3.1 - - - +
1294N VAL* 5.0 4.0 - - + +
1313N VAL* 4.1 21.5 - - + -
1314N LYS 3.8 13.7 - - - +
1315N ASP* 2.9 2.6 - - - +
1316N GLY* 2.7 29.6 + - - -
1317N ASP* 2.9 38.3 + - + +
1319N VAL* 4.0 23.1 - - + -
1325N LEU* 5.0 3.4 - - + -
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Residues in contact with ARG1282 (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* 3.6 3.1 + - + +
1281N VAL* 1.3 73.2 - - - +
1283N ILE* 1.3 77.7 + - - +
1284N GLU* 3.8 3.4 + - - +
1293N PHE* 2.9 76.8 + - + +
1295N GLU* 3.0 39.6 + - + +
1300N SER* 5.6 0.4 + - - -
1315N ASP* 3.5 4.3 - - - +
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Residues in contact with ILE1283 (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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1281N VAL* 4.2 15.9 - - + -
1282N ARG* 1.3 83.9 - - - +
1284N GLU* 1.3 60.8 + - - +
1285N GLU* 4.4 24.9 - - + +
1290N LEU* 5.6 3.1 - - + -
1291N SER 4.0 5.6 - - - +
1292N VAL* 4.5 14.8 - - + +
1311N LEU* 4.6 13.7 - - + -
1313N VAL 5.2 2.7 - - - +
1315N ASP* 3.0 37.1 + - + +
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Residues in contact with GLU1284 (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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326D GLU* 5.8 2.1 - - - +
1282N ARG* 3.8 5.5 + - - +
1283N ILE* 1.3 73.9 - - - +
1285N GLU* 1.3 60.4 + - - +
1286N THR* 2.7 31.1 + - - -
1289N LYS* 4.4 5.2 - - - +
1290N LEU* 3.4 1.8 - - - +
1291N SER* 2.9 58.0 + - - +
1293N PHE* 4.2 22.4 - - + -
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Residues in contact with GLU1285 (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* 4.0 19.6 - - + +
1284N GLU* 1.3 76.0 - - - +
1286N THR* 1.3 70.8 + - - +
1287N GLU* 4.2 3.5 + - + +
1290N LEU* 3.7 31.3 - - + +
1307N LYS 5.2 2.6 - - - +
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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