Contacts of the helix formed by residues 1400 - 1413 (chain A) in PDB entry 5XA0
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 LEU1400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1399A LEU* 1.4 79.3 - - + +
1401A PRO* 1.3 61.9 - - - +
1402A LEU 3.5 1.8 - - - +
1403A ASP* 4.0 17.1 + - + +
1404A ASP* 4.4 4.9 + - - +
1442A THR* 5.2 13.6 - - - +
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Residues in contact with PRO1401 (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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1359A ARG* 5.4 7.9 - - + +
1360A SER* 6.5 0.2 - - - -
1399A LEU* 3.3 5.4 - - - +
1400A LEU* 1.3 76.3 - - - +
1402A LEU* 1.3 66.1 + - - +
1403A ASP 3.0 4.1 + - - -
1404A ASP* 3.4 6.2 + - + +
1405A ILE* 3.2 20.7 + - - +
1442A THR* 5.9 0.2 - - - -
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Residues in contact with LEU1402 (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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1400A LEU* 3.5 1.0 - - - +
1401A PRO* 1.3 79.6 - - - +
1403A ASP* 1.3 55.5 + - - +
1405A ILE* 3.7 6.1 - - - +
1406A VAL* 2.9 30.8 + - - +
1442A THR* 3.0 36.3 - - - -
1445A HIS* 3.8 11.5 - - + +
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Residues in contact with ASP1403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1400A LEU* 4.0 12.5 + - + +
1401A PRO 3.0 0.8 + - - -
1402A LEU* 1.3 75.5 - - - +
1404A ASP* 1.3 69.0 + - - +
1406A VAL* 3.1 6.8 + - - +
1407A ARG* 3.0 22.7 + - - +
1442A THR* 5.2 1.4 - - - +
1443A SER 5.9 2.7 - - - +
1445A HIS* 5.6 4.0 - - - +
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Residues in contact with ASP1404 (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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1400A LEU 4.4 4.1 + - - +
1401A PRO* 3.4 9.3 + - + +
1403A ASP* 1.3 77.9 - - - +
1405A ILE* 1.3 65.5 + - - +
1407A ARG* 3.2 7.8 + - - +
1408A VAL* 3.0 19.0 + - - +
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Residues in contact with ILE1405 (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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1401A PRO 3.2 11.2 + - - +
1402A LEU* 3.7 11.2 - - - +
1403A ASP 3.2 0.6 - - - -
1404A ASP* 1.3 77.1 - - - +
1406A VAL* 1.3 56.1 + - - +
1408A VAL* 2.5 32.2 + - - +
1409A VAL* 3.1 11.1 + - - +
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Residues in contact with VAL1406 (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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1402A LEU 2.9 22.5 + - - +
1403A ASP* 3.1 6.0 + - - +
1405A ILE* 1.3 73.4 - - - +
1407A ARG* 1.3 62.4 + - - +
1409A VAL* 3.6 12.3 + - - +
1410A THR* 3.9 10.6 + - - -
1445A HIS* 4.7 8.7 - - - +
1447A TRP* 4.0 28.0 - - + +
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Residues in contact with ARG1407 (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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1403A ASP 3.0 12.5 + - - +
1404A ASP* 3.4 11.7 - - - +
1406A VAL* 1.3 80.4 - - - +
1408A VAL* 1.3 61.5 + - - +
1409A VAL 3.4 0.5 + - - -
1410A THR* 3.5 11.5 + - - -
1411A HIS* 3.5 13.0 + - - +
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Residues in contact with VAL1408 (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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1366A ASP 6.0 1.6 - - - +
1404A ASP 3.0 11.9 + - - +
1405A ILE* 2.5 20.9 + - - +
1407A ARG* 1.3 73.0 - - - +
1409A VAL* 1.3 61.1 + - - +
1411A HIS* 3.4 14.6 + - - +
1412A GLU* 3.7 14.7 + - - +
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Residues in contact with VAL1409 (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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1382A ALA* 6.5 0.7 - - + -
1405A ILE 3.1 8.5 + - - +
1406A VAL* 4.2 9.4 - - - +
1407A ARG 3.3 0.8 - - - -
1408A VAL* 1.3 78.7 - - - +
1410A THR* 1.3 60.7 + - - +
1411A HIS 3.6 0.5 + - - -
1412A GLU* 5.1 1.0 - - - +
1413A ASP* 3.7 18.5 + - - +
1423A ILE* 5.3 5.1 - - + +
1424A ASN* 3.7 32.5 - - + +
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Residues in contact with THR1410 (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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1406A VAL 3.9 7.6 + - - -
1407A ARG* 3.5 8.5 + - - -
1408A VAL 3.3 0.6 - - - -
1409A VAL* 1.3 77.5 - - - +
1411A HIS* 1.3 59.8 + - - +
1412A GLU 3.7 0.2 - - - -
1413A ASP* 4.6 4.9 + - - +
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Residues in contact with HIS1411 (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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1407A ARG 3.5 13.7 + - - +
1408A VAL* 3.4 9.6 + - - +
1409A VAL 3.3 1.2 - - - -
1410A THR* 1.3 79.5 - - - +
1412A GLU* 1.3 61.2 + - + +
1413A ASP* 4.9 2.0 - - - +
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Residues in contact with GLU1412 (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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1369A SER* 4.9 7.2 - - - +
1370A PRO* 4.0 32.0 - - + +
1378A VAL* 6.6 0.4 - - + -
1379A GLU* 6.5 2.0 - - + -
1408A VAL 3.7 11.4 + - - +
1409A VAL 5.1 0.2 - - - +
1411A HIS* 1.3 77.6 - - + +
1413A ASP* 1.3 75.3 + - - +
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Residues in contact with ASP1413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1379A GLU* 5.1 10.9 - - - +
1409A VAL 3.7 15.1 + - - +
1410A THR 4.6 3.6 - - - +
1411A HIS 3.7 4.0 - - - +
1412A GLU* 1.3 87.8 - - - +
1414A CYS* 1.3 70.0 + - - +
1420A ILE* 5.7 2.5 - - - -
1423A ILE* 5.2 2.7 - - - +
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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