Contacts of the helix formed by residues 1502 - 1510 (chain B) in PDB entry 1DDX
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 GLU1502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1163B MET* 5.2 10.0 - - + +
1171B LEU* 2.8 19.7 - - + +
1452B ILE* 3.0 19.9 - - - +
1455B SER* 5.4 2.8 + - - -
1456B ARG* 2.4 56.3 + - - +
1461B GLN 5.2 3.1 - - - -
1462B SER* 5.5 0.2 - - - +
1463B LEU* 3.7 1.6 - - - +
1495B TYR* 3.3 16.4 + - + +
1500B VAL 4.3 0.4 - - - +
1501B MET* 1.3 79.1 - - - +
1503B LEU* 1.3 65.5 + - - +
1505B PRO* 3.3 15.6 - - + +
1506B ALA* 3.0 25.5 + - - +
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Residues in contact with LEU1503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1380B GLU* 4.8 1.8 - - + -
1383B THR* 5.8 2.9 - - + -
1384B LEU* 3.9 18.6 - - + -
1460B TYR* 4.5 20.4 - - + -
1461B GLN 4.7 4.2 + - - +
1463B LEU* 3.3 40.6 - - + +
1466B TYR* 4.1 37.9 - - + -
1467B ARG* 6.3 0.2 - - + -
1501B MET 3.7 0.2 + - - -
1502B GLU* 1.3 67.5 - - - +
1504B TYR* 1.3 71.3 + - - +
1506B ALA* 2.9 6.1 + - - +
1507B LEU* 2.8 44.2 + - + +
1521B THR* 4.0 9.9 - - + -
1525B LEU* 4.5 8.7 - - + -
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Residues in contact with TYR1504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182B LEU* 5.1 3.6 - - + -
1383B THR* 3.6 34.8 - - + -
1384B LEU* 5.3 1.6 - - - -
1386B HIS* 3.3 26.1 + - + -
1388B HIS* 3.0 32.9 + - - -
1448B ALA* 3.6 13.2 - - + +
1451B SER* 3.2 28.3 - - - +
1452B ILE* 3.7 22.4 - - + -
1455B SER* 4.6 6.9 - - - +
1503B LEU* 1.3 79.0 - - - +
1505B PRO* 1.3 74.3 - - + +
1507B LEU* 3.0 26.5 + - + +
1508B LEU* 3.2 30.1 + - + +
1522B MET* 6.5 0.2 - - + -
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Residues in contact with PRO1505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177B VAL* 4.6 12.1 - - + -
1182B LEU* 4.7 16.8 - - + -
1452B ILE* 4.6 9.9 - - + -
1491B LEU* 5.9 0.2 - - + -
1495B TYR* 3.8 7.9 - - - +
1501B MET* 3.3 14.8 - - + -
1502B GLU* 3.3 38.1 - - + +
1503B LEU 3.2 5.2 - - - -
1504B TYR* 1.3 101.7 - - + +
1506B ALA* 1.3 55.0 + - - +
1507B LEU 2.6 12.8 + - - -
1508B LEU* 2.8 16.6 + - - +
1509B VAL* 3.1 15.3 + - + +
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Residues in contact with ALA1506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1463B LEU* 3.1 35.4 - - + -
1481B LEU* 3.3 22.0 - - + +
1501B MET* 3.2 10.2 - - + +
1502B GLU 3.0 18.1 + - - +
1503B LEU 2.9 3.0 + - - -
1505B PRO* 1.3 76.3 - - - +
1507B LEU* 1.3 51.8 + - - +
1509B VAL* 4.6 2.7 - - - -
1510B GLU* 2.6 38.1 + - - +
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Residues in contact with LEU1507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1383B THR* 5.9 0.2 - - + -
1384B LEU* 3.6 22.2 - - + +
1434B VAL* 5.6 0.7 - - - +
1435B ALA* 3.9 9.2 - - - +
1503B LEU* 2.8 46.3 + - + +
1504B TYR* 3.1 17.3 - - + +
1505B PRO 2.6 4.8 + - - -
1506B ALA* 1.3 74.5 - - - +
1508B LEU* 1.3 61.3 + - + +
1510B GLU* 3.1 24.4 - - - +
1521B THR* 3.2 27.6 - - + -
1522B MET* 3.0 49.6 - - + +
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Residues in contact with LEU1508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182B LEU* 4.0 19.1 - - + -
1386B HIS 4.1 7.4 - - - +
1387B TRP* 5.6 0.9 - - + -
1389B PRO* 3.3 14.1 - - + -
1434B VAL* 2.9 48.9 - - + +
1435B ALA 2.7 20.7 - - - +
1437B GLY* 3.3 9.9 + - - -
1438B ARG 6.2 0.2 - - - +
1440B VAL* 3.8 27.1 - - + -
1448B ALA* 5.5 0.2 - - + -
1504B TYR* 3.2 41.9 + - + +
1505B PRO 2.8 9.9 + - - +
1507B LEU* 1.3 78.3 - - + +
1509B VAL* 1.3 54.2 + - - +
1522B MET* 6.3 2.0 - - + -
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Residues in contact with VAL1509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181B VAL* 3.7 33.9 - - + +
1182B LEU* 3.7 18.2 - - + -
1435B ALA 3.3 2.9 - - - +
1436B GLY 3.7 4.2 - - - +
1437B GLY* 4.0 4.9 - - - -
1481B LEU* 5.2 3.1 - - + -
1482B THR* 3.1 33.1 - - + +
1487B MET* 4.2 12.3 - - + -
1491B LEU* 3.9 22.2 - - + -
1501B MET* 5.9 0.2 - - + -
1505B PRO* 3.1 13.8 + - + +
1506B ALA* 4.3 4.7 - - - +
1508B LEU* 1.3 73.6 - - - +
1510B GLU* 1.3 72.5 + - - +
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Residues in contact with GLU1510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435B ALA* 2.4 20.8 - - + +
1436B GLY 3.9 0.7 - - - +
1463B LEU* 6.2 0.4 - - + -
1475B TYR* 3.4 17.8 + - + +
1481B LEU* 3.2 26.9 - - + +
1506B ALA 2.6 21.8 + - - +
1507B LEU* 3.1 15.0 + - - +
1509B VAL* 1.3 84.5 - - - +
1511B LYS* 1.3 54.6 + - - +
1512B PRO* 2.7 11.0 - - - +
1519B GLY* 2.7 33.3 + - - -
1520B GLU 2.9 6.9 + - - -
1521B THR* 2.7 39.6 + - - +
1522B MET* 3.7 8.5 + - - +
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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