Contacts of the helix formed by residues 1269 - 1281 (chain A) in PDB entry 3AVR
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 PRO1269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1122A VAL* 4.4 4.7 - - + -
1124A HIS* 3.9 16.8 - - + +
1126A ILE* 4.0 10.5 - - + -
1256A TYR* 4.6 2.0 - - + -
1267A ILE 3.5 9.2 - - - +
1268A VAL* 1.3 84.0 - - + +
1270A MET* 1.3 61.4 + - - +
1271A VAL 3.2 4.1 + - - -
1272A HIS* 3.3 7.1 + - + -
1273A LEU* 2.9 26.7 + - - +
1328A ALA* 3.3 35.0 - - + -
1330A TYR* 3.4 13.9 - - + +
1337A GLU* 3.3 17.3 - - - +
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Residues in contact with MET1270 (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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1118A LEU* 5.8 0.9 - - + -
1150A ASN* 4.3 3.1 - - - +
1152A PHE* 4.1 4.9 - - + -
1249A TYR* 3.9 31.9 - - + -
1252A ALA* 3.8 33.7 - - + +
1253A VAL* 4.2 11.4 - - + -
1256A TYR* 3.5 41.6 - - + -
1268A VAL* 2.9 34.2 + - - +
1269A PRO* 1.3 72.3 - - - +
1271A VAL* 1.3 58.0 + - - +
1273A LEU* 3.9 17.3 - - + +
1274A SER* 2.7 33.5 + - - +
1295A CYS* 4.7 1.5 - - - -
1337A GLU* 3.3 3.2 + - - -
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Residues in contact with VAL1271 (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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1256A TYR* 3.4 26.5 - - + +
1260A LYS* 6.1 0.7 - - - +
1270A MET* 1.3 75.6 - - - +
1272A HIS* 1.3 66.2 + - - +
1274A SER* 3.0 14.4 + - - -
1275A TRP* 3.1 26.9 + - + +
1295A CYS* 4.8 6.7 - - - -
1299A THR* 3.8 30.7 - - + -
1337A GLU* 3.1 11.4 + - - +
1339A PHE* 3.5 36.6 - - + -
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Residues in contact with HIS1272 (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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1122A VAL* 2.7 31.3 + - + -
1123A GLY* 5.0 0.8 - - - -
1124A HIS* 3.6 24.6 + + - -
1269A PRO* 3.5 13.2 - - + +
1271A VAL* 1.3 76.2 - - - +
1273A LEU* 1.3 64.6 + - - +
1275A TRP* 3.4 3.6 + - - +
1276A ASN* 3.2 31.6 + - - +
1322A ARG* 4.0 22.2 + - - -
1326A GLU 4.4 2.7 - - - -
1328A ALA* 4.1 13.8 - - + +
1337A GLU* 2.9 20.4 + - - +
1339A PHE* 4.1 15.0 - - + -
1378A TYR* 3.6 23.8 + - - -
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Residues in contact with LEU1273 (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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1118A LEU* 3.3 32.1 - - + +
1119A LEU* 5.0 0.2 - - + -
1121A HIS* 3.7 24.7 - - + -
1122A VAL* 3.7 13.9 - - + +
1152A PHE* 4.3 10.1 - - + -
1268A VAL* 3.9 22.9 - - + -
1269A PRO* 2.9 18.5 + - + +
1270A MET* 4.0 21.8 - - + +
1272A HIS* 1.3 83.0 - - + +
1274A SER* 1.3 57.1 + - - +
1276A ASN* 3.2 3.8 + - - +
1277A MET* 2.8 43.6 + - + +
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Residues in contact with SER1274 (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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1249A TYR* 2.7 36.4 + - - -
1253A VAL* 5.4 0.2 - - - +
1270A MET* 2.7 22.7 + - - +
1271A VAL 3.0 5.2 + - - -
1273A LEU* 1.3 76.2 - - - +
1275A TRP* 1.3 57.6 + - - +
1277A MET* 3.3 12.6 + - - +
1278A ALA* 2.9 28.1 + - - +
1292A ILE* 4.2 6.1 - - - +
1295A CYS* 3.7 17.3 - - - -
1296A LEU* 3.9 10.7 - - - +
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Residues in contact with TRP1275 (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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1271A VAL* 3.1 29.3 + - + +
1272A HIS 3.8 6.3 - - - +
1274A SER* 1.3 77.9 - - - +
1276A ASN* 1.3 57.2 + - - +
1278A ALA* 3.2 4.5 + - - +
1279A ARG* 3.0 37.3 + - - +
1295A CYS* 5.5 0.6 - - - -
1296A LEU* 3.5 43.1 - - + +
1299A THR* 3.0 20.5 + - - -
1300A LEU* 4.0 21.3 - - + -
1339A PHE* 3.5 34.4 - + + -
1378A TYR* 6.1 2.2 - - + +
1383A LEU* 3.2 54.5 - - + -
1386A VAL* 3.9 20.0 - - + +
1387A TYR* 4.1 17.7 - - + -
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Residues in contact with ASN1276 (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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1121A HIS* 3.0 28.1 + - - +
1122A VAL 3.1 19.4 + - - -
1123A GLY* 4.3 4.0 - - - +
1272A HIS* 3.2 27.4 + - - +
1273A LEU 3.2 7.4 + - - +
1275A TRP* 1.3 72.9 - - - +
1277A MET* 1.3 60.7 + - - +
1279A ARG* 3.0 21.4 + - - +
1280A ASN* 2.9 43.1 + - - +
1322A ARG* 5.9 0.6 - - - +
1378A TYR* 5.5 1.9 + - - -
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Residues in contact with MET1277 (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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1118A LEU* 3.8 30.1 - - + -
1121A HIS* 4.6 3.8 - - + +
1244A LEU* 4.7 6.3 - - + -
1249A TYR* 3.9 26.0 - - + -
1273A LEU* 2.8 42.7 + - + +
1274A SER* 3.4 10.1 - - - +
1276A ASN* 1.3 75.2 - - - +
1278A ALA* 1.3 57.9 + - - +
1280A ASN* 4.9 0.2 - - - -
1281A ILE* 2.9 57.0 + - + +
1288A LEU* 5.1 1.6 - - + -
1292A ILE* 3.5 38.1 - - + -
1390A PHE* 4.5 2.1 - - - -
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Residues in contact with ALA1278 (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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1274A SER 2.9 11.5 + - - +
1275A TRP 3.4 9.4 - - - +
1276A ASN 3.1 0.4 - - - -
1277A MET* 1.3 76.8 - - - +
1279A ARG* 1.3 62.7 + - - +
1281A ILE 4.6 2.8 - - - +
1292A ILE* 4.9 1.1 - - + +
1296A LEU* 3.6 32.3 - - + -
1386A VAL* 3.7 17.6 - - + +
1389A GLN 5.3 1.6 - - - +
1390A PHE* 3.6 32.7 + - + +
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Residues in contact with ARG1279 (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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1275A TRP* 3.0 21.5 + - - +
1276A ASN* 3.0 26.0 + - - +
1278A ALA* 1.3 79.9 - - - +
1280A ASN* 1.3 70.5 + - - +
1378A TYR* 3.8 24.8 - - - -
1382A ASP* 2.8 41.8 + - - -
1383A LEU* 4.5 8.5 - - - +
1386A VAL* 3.4 29.7 - - + +
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Residues in contact with ASN1280 (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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1A EDO 5.2 3.4 + - - -
1121A HIS* 3.3 39.0 + - + +
1276A ASN* 2.9 28.4 + - - +
1279A ARG* 1.3 91.6 - - - +
1281A ILE* 1.3 60.1 + - + +
1282A LYS* 4.2 2.4 + - - +
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Residues in contact with ILE1281 (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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1115A ALA 4.9 3.8 - - - +
1118A LEU* 4.4 2.9 - - + -
1121A HIS* 3.6 42.2 - - + +
1244A LEU* 3.8 39.7 - - + -
1277A MET* 2.9 37.0 + - + +
1278A ALA 4.6 2.3 + - - +
1279A ARG 3.8 0.8 - - - -
1280A ASN* 1.3 82.3 - - + +
1282A LYS* 1.3 70.0 + - - +
1283A VAL* 3.5 18.2 + - + -
1390A PHE* 3.8 16.5 - - - -
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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