Contacts of the strand formed by residues 1269 - 1276 (chain A) in PDB entry 2VZ9
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 ASP1269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1240A PRO 3.2 6.9 + - - +
1241A LYS* 3.9 26.5 - - + +
1242A MET 3.0 28.2 + - - +
1268A MET* 1.3 81.7 - - - +
1270A LEU* 1.3 61.2 + - - +
1271A ASP* 4.2 10.7 + - - +
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Residues in contact with LEU1270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A MET* 3.6 18.8 - - + +
1244A VAL* 3.8 13.0 - - + -
1258A ILE 4.5 0.2 - - - +
1259A PRO* 3.7 37.5 - - + -
1262A LEU* 3.4 33.4 - - + -
1263A ASN* 4.4 15.9 - - - +
1268A MET* 5.0 5.2 - - + -
1269A ASP* 1.3 77.6 + - - +
1271A ASP* 1.3 65.9 + - - +
1272A TYR* 3.8 17.2 + - + +
1292A LEU 5.7 2.9 - - - +
1293A HIS* 4.9 5.9 - - - +
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Residues in contact with ASP1271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A MET 3.4 7.8 + - - +
1243A LYS* 3.8 34.2 - - + +
1244A VAL 2.9 27.1 + - - +
1269A ASP* 4.2 8.9 + - - +
1270A LEU* 1.3 75.9 - - - +
1272A TYR* 1.3 60.7 + - - +
1273A THR* 4.1 4.7 + - - +
1295A THR* 5.6 4.7 - - - +
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Residues in contact with TYR1272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244A VAL* 3.3 40.4 - - + -
1245A VAL 5.1 0.2 - - - -
1246A GLU* 3.1 36.7 + - + +
1254A LEU* 3.5 15.6 + - - +
1255A TYR* 3.3 28.3 - - + -
1258A ILE* 4.4 16.3 - - + +
1259A PRO* 4.1 14.8 - - + -
1270A LEU* 3.7 20.3 + - + -
1271A ASP* 1.3 72.5 - - - +
1273A THR* 1.3 60.6 + - - +
1274A ALA* 5.1 2.0 - - + -
1292A LEU 5.5 0.7 - - - +
1293A HIS 4.2 7.4 + - - +
1294A VAL* 3.2 42.7 - - + -
1295A THR* 2.6 33.3 + - - -
1316A VAL* 4.5 1.0 - - - +
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Residues in contact with THR1273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244A VAL 3.2 16.7 + - - -
1245A VAL* 3.4 14.5 - - + +
1246A GLU* 3.0 26.5 + - - +
1271A ASP* 4.1 5.9 + - - +
1272A TYR* 1.3 81.9 + - - +
1274A ALA* 1.3 59.5 + - - +
1275A THR* 4.1 13.0 - - + +
1294A VAL* 3.9 0.7 - - - -
1295A THR* 2.9 32.8 + - + +
1296A GLN* 4.9 4.7 - - - -
1297A GLY* 6.0 0.2 - - - -
1308A SER 4.6 14.6 - - - +
1309A LEU* 4.6 2.7 - - + -
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Residues in contact with ALA1274 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246A GLU* 4.1 6.5 - - - +
1249A ALA* 4.1 16.4 - - + -
1255A TYR* 4.7 9.9 - - + -
1272A TYR* 5.1 1.1 - - + -
1273A THR* 1.3 69.7 - - - +
1275A THR* 1.3 59.5 + - - +
1282A LEU* 3.6 17.6 - - + +
1289A LEU* 4.0 21.8 - - + -
1294A VAL* 3.4 17.8 - - + +
1295A THR 2.7 10.5 + - - +
1296A GLN* 3.7 4.1 - - - -
1297A GLY 3.7 13.5 + - - -
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Residues in contact with THR1275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245A VAL* 3.6 24.4 - - - +
1246A GLU 3.3 19.1 + - - +
1247A VAL* 3.7 4.6 - - - +
1248A LEU 3.6 9.0 + - - -
1249A ALA* 3.9 0.4 + - - -
1273A THR* 3.8 8.1 + - + +
1274A ALA* 1.3 72.6 - - - +
1276A ASP* 1.3 68.0 - - - +
1297A GLY* 3.3 29.6 - - - +
1298A GLN 3.4 3.8 - - - +
1299A TRP* 3.2 43.7 - - + +
1308A SER 6.0 1.1 - - - +
1309A LEU* 4.3 4.6 - - + +
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Residues in contact with ASP1276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248A LEU* 3.4 7.0 - - - +
1249A ALA* 2.5 28.7 + - - -
1250A GLY* 2.7 31.8 + - - -
1274A ALA 4.0 0.4 + - - -
1275A THR* 1.3 72.8 - - - +
1277A ARG* 1.3 68.3 + - - +
1278A ASN 3.1 7.4 + - - +
1281A ALA* 3.0 17.6 - - + +
1282A LEU* 3.7 24.6 - - + +
1297A GLY 3.3 6.9 + - - -
1298A GLN* 3.1 22.2 - - - +
1299A TRP 3.6 5.8 - - - -
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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