Contacts of the helix formed by residues 1331 - 1339 (chain D) in PDB entry 4OIO
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 ASP1331 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1267D ARG* 2.7 52.7 + - + +
1268D PRO* 4.1 5.2 - - + -
1271D LYS* 3.6 25.7 + - + +
1272D ALA 4.9 0.8 + - - -
1329D ALA 3.6 3.6 + - - -
1330D ILE* 1.3 76.7 - - - +
1332D PRO* 1.3 74.0 - - - +
1333D HIS* 3.1 15.1 + - - -
1334D GLN* 3.2 28.1 + - - +
1335D LEU 3.1 17.2 + - - -
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Residues in contact with PRO1332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261D GLU 5.8 0.9 - - - +
1262D LEU* 5.4 4.3 - - + +
1265D ALA* 4.5 13.0 - - + +
1266D ARG 3.7 19.7 - - - +
1268D PRO* 4.7 1.1 - - + -
1330D ILE* 3.2 11.2 - - + +
1331D ASP* 1.3 92.9 - - - +
1333D HIS* 1.3 58.0 + - - +
1335D LEU* 3.4 8.8 + - + +
1336D LEU* 2.9 26.0 + - - +
1344D VAL* 3.6 11.1 - - + +
1347D TYR* 4.9 7.9 - - + -
1348D LEU* 4.4 21.3 - - + -
1421D LEU* 3.5 24.2 - - + +
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Residues in contact with HIS1333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1265D ALA* 3.0 37.8 + - + +
1267D ARG* 3.7 35.7 + - - +
1331D ASP* 3.1 11.0 + - - +
1332D PRO* 1.3 74.8 - - + +
1334D GLN* 1.3 60.6 + - - +
1336D LEU* 2.9 23.8 + - + +
1337D GLU* 2.9 21.5 + - + +
1420D LEU* 5.8 4.3 - - + -
1421D LEU* 2.8 39.3 + - + +
1422D MET* 4.8 1.2 - - - -
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Residues in contact with GLN1334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267D ARG* 5.0 4.4 - - - +
1271D LYS* 4.1 21.0 - - - +
1272D ALA 4.1 12.6 - - - +
1273D VAL* 5.1 1.0 - - - +
1274D ILE* 3.8 27.7 + - + +
1330D ILE* 5.8 0.2 - - - +
1331D ASP* 3.2 30.5 + - - +
1333D HIS* 1.3 76.9 - - - +
1335D LEU* 1.3 57.7 + - - +
1337D GLU* 3.3 13.8 + - - +
1338D ALA* 2.9 32.6 + - - +
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Residues in contact with LEU1335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274D ILE* 3.8 6.4 - - + +
1322D GLY* 4.0 22.2 - - - +
1330D ILE* 4.0 19.7 - - + -
1331D ASP 3.1 12.5 + - - +
1332D PRO* 3.5 10.1 - - + +
1334D GLN* 1.3 77.2 - - - +
1336D LEU* 1.3 56.2 + - - +
1338D ALA 4.6 0.2 - - - +
1339D LYS* 2.9 57.6 + - + +
1340D GLY 3.0 6.4 + - - -
1343D ALA* 4.0 12.8 - - + +
1344D VAL* 3.8 10.8 - - + +
1347D TYR* 3.6 40.2 - - + -
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Residues in contact with LEU1336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332D PRO 2.9 14.2 + - - +
1333D HIS* 2.9 13.6 + - + +
1335D LEU* 1.3 77.7 - - - +
1337D GLU* 1.3 64.9 + - + +
1340D GLY* 3.2 18.9 - - - +
1341D PRO* 3.7 18.5 - - + +
1344D VAL* 3.5 20.2 - - + +
1376D MET* 3.7 29.2 - - + -
1419D PRO* 3.2 37.6 - - + +
1420D LEU* 4.1 0.9 - - + -
1421D LEU* 3.6 26.2 - - + +
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Residues in contact with GLU1337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1333D HIS* 2.9 17.7 + - + +
1334D GLN* 3.3 14.1 + - - +
1336D LEU* 1.3 82.0 - - + +
1338D ALA* 1.3 62.8 + - - +
1339D LYS 4.9 0.3 - - - -
1340D GLY* 4.8 0.5 + - - -
1418D LYS* 3.8 26.0 + - - +
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Residues in contact with ALA1338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274D ILE* 4.3 5.2 - - + -
1275D SER 3.8 22.4 - - - +
1276D GLU* 4.3 18.7 - - + +
1321D ALA* 4.2 14.1 - - - +
1322D GLY* 3.9 13.7 - - - +
1334D GLN 2.9 16.2 + - - +
1335D LEU* 4.6 0.4 - - - +
1337D GLU* 1.3 80.0 - - - +
1339D LYS* 1.3 60.6 + - - +
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Residues in contact with LYS1339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320D GLU* 4.7 19.1 - - - +
1321D ALA* 3.0 28.1 + - + +
1322D GLY* 4.8 5.0 + - - -
1323D GLN* 5.2 1.8 - - - +
1335D LEU* 2.9 31.8 + - + +
1336D LEU 4.3 0.2 - - - -
1337D GLU 4.9 0.4 - - - -
1338D ALA* 1.3 79.8 - - + +
1340D GLY* 1.3 60.6 + - - +
1342D GLU* 4.9 3.1 - - - +
1343D ALA* 3.3 26.2 - - + +
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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