Contacts of the helix formed by residues 1331 - 1340 (chain N) in PDB entry 5D4D
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1267N ARG* 3.0 33.7 + - - +
1268N PRO* 3.9 7.0 - - + -
1271N LYS* 3.0 30.1 + - + +
1272N ALA 5.3 1.4 + - - -
1329N ALA 3.6 4.2 + - - -
1330N ILE* 1.3 76.1 - - - +
1332N PRO* 1.3 72.1 - - - +
1333N HIS* 3.0 24.9 + - - +
1334N GLN* 3.1 33.4 + - - +
1335N LEU 3.1 17.0 + - - -
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Residues in contact with PRO1332 (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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1261N GLU 5.9 0.4 - - - +
1262N LEU* 5.2 5.4 - - + -
1265N ALA* 4.7 8.1 - - + -
1266N ARG 3.8 20.9 - - - +
1268N PRO* 4.4 2.5 - - + -
1330N ILE* 3.1 11.4 - - + +
1331N ASP* 1.3 88.3 - - - +
1333N HIS* 1.3 59.8 + - + +
1335N LEU* 3.3 8.3 + - + +
1336N LEU* 2.9 27.9 + - - +
1344N VAL* 4.0 11.8 - - + +
1347N TYR* 4.8 8.7 - - + -
1348N LEU* 4.3 20.4 - - + -
1421N LEU* 3.6 24.5 - - + -
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Residues in contact with HIS1333 (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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1265N ALA* 2.7 37.3 + - + +
1267N ARG* 3.5 41.0 + - + +
1331N ASP* 3.0 11.9 + - - +
1332N PRO* 1.3 77.5 - - + +
1334N GLN* 1.3 60.0 - - - +
1336N LEU* 3.3 10.0 + - + +
1337N GLU* 3.0 31.7 + - - +
1420N LEU* 6.3 0.8 - - - +
1421N LEU* 2.9 38.1 + - + +
1422N MET* 4.8 1.8 - - - -
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Residues in contact with GLN1334 (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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1267N ARG* 5.5 3.3 - - - +
1271N LYS* 3.2 33.7 - - - +
1272N ALA 4.6 5.2 - - - +
1273N VAL* 5.3 1.6 - - - +
1274N ILE* 3.7 26.3 + - + +
1330N ILE* 5.8 0.2 - - - +
1331N ASP* 3.1 31.2 + - - +
1333N HIS* 1.3 74.7 - - + +
1335N LEU* 1.3 61.3 + - - +
1337N GLU* 3.2 11.8 + - - +
1338N ALA* 2.9 30.7 + - - +
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Residues in contact with LEU1335 (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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1274N ILE* 3.7 8.2 - - + +
1322N GLY* 3.6 28.0 - - - +
1330N ILE* 3.9 16.4 - - + -
1331N ASP 3.1 11.9 + - - +
1332N PRO* 3.6 9.6 - - + +
1334N GLN* 1.3 76.6 - - - +
1336N LEU* 1.3 58.1 + - - +
1338N ALA* 4.5 0.7 - - - +
1339N LYS* 2.9 46.8 + - + +
1340N GLY 3.4 4.0 + - - +
1343N ALA* 4.1 16.6 - - + +
1344N VAL* 4.3 7.4 - - + +
1347N TYR* 3.7 40.8 - - + -
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Residues in contact with LEU1336 (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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1332N PRO 2.9 17.8 + - - +
1333N HIS* 3.5 10.1 - - - +
1334N GLN 3.1 0.2 - - - -
1335N LEU* 1.3 77.2 - - - +
1337N GLU* 1.3 64.0 + - + +
1340N GLY* 3.0 22.8 + - - +
1341N PRO* 3.5 29.2 - - + -
1344N VAL* 3.4 18.6 - - + +
1376N MET* 4.1 4.9 - - + -
1419N PRO* 3.6 36.8 - - + +
1420N LEU* 3.9 3.6 - - + -
1421N LEU* 3.5 38.4 - - + +
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Residues in contact with GLU1337 (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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1333N HIS 3.0 17.1 + - - +
1334N GLN* 3.2 12.9 + - - +
1336N LEU* 1.3 78.5 - - + +
1338N ALA* 1.3 62.6 + - - +
1340N GLY 4.8 0.2 + - - -
1418N LYS* 5.0 17.5 + - + -
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Residues in contact with ALA1338 (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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1274N ILE* 4.4 6.3 - - + -
1275N SER 4.2 7.9 - - - +
1276N GLU* 4.7 15.0 - - + +
1321N ALA* 4.6 11.5 - - - +
1322N GLY* 4.0 26.0 - - - +
1334N GLN 2.9 15.8 + - - +
1335N LEU 4.0 1.1 - - - +
1337N GLU* 1.3 80.5 - - - +
1339N LYS* 1.3 61.9 + - - +
1340N GLY 3.5 0.6 + - - -
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Residues in contact with LYS1339 (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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1320N GLU* 5.8 6.8 - - + +
1321N ALA* 3.7 22.9 - - - +
1322N GLY* 4.4 5.5 + - - +
1323N GLN* 6.3 0.2 - - - +
1335N LEU* 2.9 26.9 + - + +
1338N ALA* 1.3 73.5 - - - +
1340N GLY* 1.3 62.7 + - - +
1342N GLU* 5.4 0.9 - - - +
1343N ALA* 3.6 26.5 + - + +
1346N ARG* 4.7 12.3 - - - +
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Residues in contact with GLY1340 (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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1335N LEU 3.4 1.0 + - - +
1336N LEU* 3.0 24.5 + - - -
1338N ALA 3.5 1.6 + - - -
1339N LYS* 1.3 78.6 - - - +
1341N PRO* 1.3 75.7 - - - +
1342N GLU* 3.5 2.7 - - - -
1343N ALA* 3.2 12.8 + - - +
1344N VAL* 3.2 14.7 + - - +
1419N PRO* 5.7 0.7 - - - -
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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