Contacts of the helix formed by residues 1401 - 1411 (chain B) 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 PRO1401 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388B LYS* 5.3 13.7 - - + -
1398B SER* 5.4 6.1 - - - -
1400B LEU* 1.3 74.9 - - - +
1402B LEU* 1.3 61.6 + - - +
1403B ASP 3.4 2.6 + - - -
1404B ASP* 4.0 11.7 + - + +
1405B ILE* 4.1 11.4 + - - +
1441B TYR* 4.8 13.9 - - + -
1442B THR* 2.8 12.7 - - - -
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Residues in contact with LEU1402 (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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1401B PRO* 1.3 77.8 - - - +
1403B ASP* 1.3 62.5 + - - +
1405B ILE* 3.6 6.0 + - - +
1406B VAL* 3.3 21.5 + - - +
1441B TYR 4.9 1.7 + - - +
1442B THR* 3.7 6.8 - - - -
1444B ASN 4.2 6.3 - - - +
1445B HIS* 3.7 33.7 - - + -
1446B MET 5.4 0.7 - - - +
1448B LYS* 5.6 6.5 - - + +
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Residues in contact with ASP1403 (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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1400B LEU* 5.7 4.0 - - + +
1401B PRO 3.4 1.0 - - - -
1402B LEU* 1.3 77.5 - - - +
1404B ASP* 1.3 59.9 + - - +
1406B VAL* 3.2 6.8 + - - +
1407B ARG* 2.9 31.2 + - - +
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Residues in contact with ASP1404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366B ASP* 6.3 2.9 - - + -
1401B PRO* 4.0 7.9 + - + +
1402B LEU 3.5 0.4 - - - -
1403B ASP* 1.3 79.4 - - - +
1405B ILE* 1.3 57.8 + - - +
1407B ARG* 4.0 4.6 - - - +
1408B VAL* 2.9 31.4 + - - +
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Residues in contact with ILE1405 (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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1401B PRO 4.1 9.2 + - - +
1402B LEU* 3.6 8.4 + - - +
1403B ASP 3.2 0.4 - - - -
1404B ASP* 1.3 78.3 - - - +
1406B VAL* 1.4 59.8 + - - +
1408B VAL* 3.9 3.4 - - - -
1409B VAL* 2.8 32.1 + - - +
1427B ASN* 5.2 14.4 - - + +
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Residues in contact with VAL1406 (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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1402B LEU 3.3 15.0 + - - +
1403B ASP* 3.2 8.5 + - - +
1405B ILE* 1.4 76.7 - - - +
1407B ARG* 1.3 57.6 + - - +
1409B VAL* 3.9 4.8 - - - +
1410B THR* 3.1 30.5 + - - -
1447B TRP* 5.3 17.7 - - + +
1448B LYS* 5.8 2.7 - - - +
1451B GLU* 5.8 7.4 - - + -
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Residues in contact with ARG1407 (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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1403B ASP 2.9 16.8 + - - +
1404B ASP* 4.0 5.8 - - - +
1406B VAL* 1.3 74.8 - - - +
1408B VAL* 1.3 59.9 + - - +
1409B VAL 3.2 0.4 - - - -
1410B THR* 5.6 0.7 - - - -
1411B HIS* 2.8 37.1 + - + +
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Residues in contact with VAL1408 (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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1366B ASP* 5.0 11.7 - - + +
1404B ASP 2.9 19.6 + - - +
1405B ILE* 4.5 3.8 - - - +
1407B ARG* 1.3 75.8 - - - +
1409B VAL* 1.4 58.6 + - - +
1410B THR 3.7 0.2 - - - -
1411B HIS* 4.1 13.9 - - - +
1412B GLU* 5.9 0.7 - - - +
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Residues in contact with VAL1409 (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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1405B ILE 2.8 21.8 + - - +
1406B VAL* 3.9 6.5 - - - +
1407B ARG 3.2 0.2 - - - -
1408B VAL* 1.4 78.6 - - - +
1410B THR* 1.3 58.6 + - - +
1411B HIS 3.6 0.2 - - - -
1420B ILE* 4.2 19.2 - - - +
1424B ASN* 4.6 21.0 - - + +
1427B ASN* 5.9 5.8 - - + -
1451B GLU* 6.4 1.8 - - + -
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Residues in contact with THR1410 (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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1406B VAL 3.1 16.6 + - - -
1407B ARG* 4.1 0.9 - - - -
1409B VAL* 1.3 74.3 - - - +
1411B HIS* 1.4 57.5 + - - +
1412B GLU* 4.1 2.3 + - - -
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Residues in contact with HIS1411 (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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1368B ASN 4.0 14.1 - - - +
1369B SER* 4.8 3.1 - - - -
1407B ARG* 2.8 23.0 + - + +
1408B VAL* 4.1 13.1 - - - +
1409B VAL 3.6 2.8 - - - -
1410B THR* 1.4 74.9 - - - +
1412B GLU* 1.3 59.9 + - - +
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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