Contacts of the helix formed by residues 1334 - 1344 (chain A) in PDB entry 2XBA
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 SER1334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1294A LYS* 4.5 2.0 - - - +
1332A SER 4.0 0.6 + - - -
1333A LYS* 1.3 76.0 - - - +
1335A ASN* 1.3 66.4 + - - +
1336A GLN* 3.7 5.6 + - - +
1337A GLU* 3.0 35.1 + - - +
1338A VAL* 2.9 22.7 + - - +
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Residues in contact with ASN1335 (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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1289A ALA* 4.2 18.2 + - - +
1291A LEU 4.1 15.9 + - - -
1293A VAL* 3.6 29.3 + - + +
1294A LYS* 3.5 26.6 + - - +
1334A SER* 1.3 73.5 - - - +
1336A GLN* 1.3 57.8 + - - +
1338A VAL* 3.2 7.1 + - - +
1339A LEU* 2.9 27.9 + - - +
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Residues in contact with GLN1336 (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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1334A SER* 3.3 5.7 + - - +
1335A ASN* 1.3 79.5 - - - +
1337A GLU* 1.3 62.2 + - + +
1339A LEU* 3.2 27.8 + - - +
1340A GLU* 2.9 56.9 + - - +
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Residues in contact with GLU1337 (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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1332A SER 3.6 6.8 - - - +
1333A LYS* 3.4 21.7 - - + +
1334A SER* 3.0 38.0 + - - +
1336A GLN* 1.3 77.1 - - + +
1338A VAL* 1.3 63.7 + - - +
1340A GLU* 3.4 9.0 + - - +
1341A PHE* 2.9 24.8 + - - +
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Residues in contact with VAL1338 (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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1293A VAL* 4.6 6.7 - - + +
1294A LYS* 4.0 24.9 - - + -
1301A PHE* 5.5 0.9 - - + -
1330A TYR* 3.4 55.9 - - + -
1333A LYS* 3.5 12.6 - - + +
1334A SER 2.9 17.8 + - - +
1335A ASN* 3.5 7.9 - - - +
1337A GLU* 1.3 76.8 - - - +
1339A LEU* 1.3 64.8 + - - +
1341A PHE* 3.1 6.1 + - - +
1342A VAL* 2.9 34.1 + - + +
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Residues in contact with LEU1339 (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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1293A VAL* 4.4 10.3 - - + +
1301A PHE* 4.0 45.8 - - + -
1335A ASN 2.9 13.5 + - - +
1336A GLN* 3.5 36.8 - - - +
1338A VAL* 1.3 76.6 - - - +
1340A GLU* 1.3 56.7 + - + +
1342A VAL* 4.1 0.5 - - - +
1343A THR* 2.8 51.7 + - + +
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Residues in contact with GLU1340 (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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1336A GLN* 2.9 49.9 + - - +
1337A GLU* 4.0 7.5 - - - +
1339A LEU* 1.3 75.5 - - + +
1341A PHE* 1.3 64.4 + - - +
1343A THR* 3.4 7.2 + - - -
1344A SER* 3.0 29.4 + - - +
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Residues in contact with PHE1341 (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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1330A TYR* 3.8 29.2 - + - -
1333A LYS* 3.7 29.6 - - - -
1337A GLU 2.9 19.3 + - - +
1338A VAL* 3.4 4.5 - - - +
1340A GLU* 1.3 75.7 - - - +
1342A VAL* 1.3 62.1 + - + +
1344A SER* 3.0 13.3 + - - -
1345A GLY 3.4 0.2 + - - -
1346A GLY* 2.9 47.9 + - - -
1347A ARG* 3.4 33.0 - - - -
1348A MET* 4.1 1.1 - - - -
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Residues in contact with VAL1342 (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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1296A MET 4.6 1.6 - - - +
1298A PRO* 3.8 19.1 - - + +
1301A PHE* 4.4 16.6 - - + -
1313A TRP* 3.6 31.2 - - + -
1330A TYR* 3.4 37.7 - - + +
1338A VAL* 2.9 24.2 + - + +
1339A LEU 4.2 1.6 - - - +
1341A PHE* 1.3 78.3 - - + +
1343A THR* 1.3 63.2 + - - +
1345A GLY* 3.1 11.4 + - - -
1346A GLY 3.7 13.0 - - - +
1347A ARG* 3.1 12.9 + - - +
1368A HIS* 5.1 1.7 + - - -
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Residues in contact with THR1343 (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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1298A PRO* 4.2 19.7 - - + -
1301A PHE* 4.0 23.8 - - + -
1302A MET* 4.5 19.5 - - + -
1339A LEU* 2.8 32.4 + - + +
1340A GLU* 3.4 11.1 + - - -
1342A VAL* 1.3 76.8 - - - +
1344A SER* 1.3 58.8 + - - +
1345A GLY 3.4 0.6 + - - -
1368A HIS* 5.0 9.6 + - - -
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Residues in contact with SER1344 (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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1340A GLU* 3.0 18.2 + - - +
1341A PHE* 3.0 7.4 + - - -
1343A THR* 1.3 79.1 + - - +
1345A GLY* 1.3 57.7 + - - +
1346A GLY 3.4 1.7 + - - -
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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