Contacts of the helix formed by residues 1444 - 1453 (chain A) in PDB entry 5XJY
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 THR1444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1441A VAL* 4.5 7.3 - - - +
1442A PRO* 2.6 24.5 + - + +
1443A GLN* 1.3 78.6 - - - +
1445A ILE* 1.3 59.7 + - - +
1446A MET 3.3 2.0 - - - +
1447A ASP* 3.2 29.7 - - + +
1448A LEU* 2.9 20.8 + - - +
1481A ALA* 5.5 6.3 - - - +
1484A LEU* 4.3 11.8 - - - +
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Residues in contact with ILE1445 (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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1441A VAL* 3.7 33.7 - - + +
1442A PRO 4.3 2.5 - - - +
1443A GLN* 3.8 20.4 - - - +
1444A THR* 1.3 75.9 - - - +
1446A MET* 1.3 65.0 + - + +
1447A ASP 3.2 0.4 - - - -
1448A LEU* 3.4 21.3 - - + +
1449A PHE* 2.9 23.7 + - - +
1484A LEU* 5.9 0.9 - - + -
1485A PRO* 6.6 0.2 - - + -
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Residues in contact with MET1446 (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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1443A GLN* 3.4 29.4 - - + +
1444A THR* 3.3 0.6 - - - -
1445A ILE* 1.3 78.2 - - + +
1447A ASP* 1.3 58.6 + - - +
1448A LEU 3.2 0.2 - - - -
1449A PHE* 3.6 11.0 - - + +
1450A GLN* 2.9 33.5 + - + +
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Residues in contact with ASP1447 (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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1444A THR* 3.2 35.7 + - + +
1445A ILE 3.2 0.4 - - - -
1446A MET* 1.3 79.5 - - - +
1448A LEU* 1.3 51.2 + - - +
1450A GLN* 3.5 6.9 - - - +
1451A ASN* 2.4 49.5 + - - +
1480A GLY* 6.1 1.2 - - - -
1484A LEU* 5.9 0.8 - - - +
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Residues in contact with LEU1448 (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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1444A THR 2.9 9.4 + - - +
1445A ILE* 3.5 22.2 - - + +
1446A MET 3.2 0.4 - - - -
1447A ASP* 1.3 77.8 - - - +
1449A PHE* 1.3 58.2 + - - +
1451A ASN* 3.1 10.6 + - + +
1452A GLY* 2.8 22.6 + - - +
1484A LEU* 3.6 35.0 - - + -
1485A PRO* 3.6 29.8 - - + -
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Residues in contact with PHE1449 (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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1445A ILE 2.9 16.9 + - - +
1446A MET* 3.2 12.9 + - + +
1448A LEU* 1.3 76.1 - - - +
1450A GLN* 1.3 89.5 + - + +
1451A ASN 3.2 0.2 - - - -
1452A GLY* 2.9 17.2 + - - +
1453A ASN 3.0 8.7 + - - -
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Residues in contact with GLN1450 (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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1446A MET* 2.9 18.8 + - + +
1447A ASP* 3.5 10.0 - - - +
1449A PHE* 1.3 107.4 - - + +
1451A ASN* 1.3 56.1 + - - +
1453A ASN* 2.8 52.1 - - - +
2305A NAG 3.9 23.9 + - + +
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Residues in contact with ASN1451 (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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1447A ASP* 2.4 42.1 + - - +
1448A LEU* 3.1 19.0 + - + +
1450A GLN* 1.3 76.5 - - - +
1452A GLY* 1.3 57.1 + - - +
1453A ASN 3.1 4.5 - - - -
1455A THR* 2.2 64.1 + - - +
1460A SER 6.1 1.1 - - - -
1461A PRO 5.2 6.8 - - - +
1462A ALA* 5.3 1.4 + - - +
1484A LEU* 3.3 24.4 - - + +
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Residues in contact with GLY1452 (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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1448A LEU* 2.8 14.0 + - - +
1449A PHE* 2.9 9.7 + - - -
1451A ASN* 1.3 74.3 - - - +
1453A ASN* 1.3 59.3 + - - +
1454A TRP 3.6 2.4 + - - -
1455A THR 4.2 7.6 + - - +
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Residues in contact with ASN1453 (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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1449A PHE 3.0 6.1 + - - -
1450A GLN* 2.8 51.3 - - - +
1451A ASN* 3.0 9.4 - - - +
1452A GLY* 1.3 75.6 - - - +
1454A TRP* 1.3 83.3 + - - +
1455A THR* 3.1 3.8 + - - +
2305A NAG 1.5 68.7 + - + +
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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