Contacts of the helix formed by residues 1392 - 1399 (chain A) in PDB entry 5A31
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 THR1392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1390A PRO 3.3 3.0 - - - +
1391A ASP* 1.3 82.8 - - - +
1393A MET* 1.3 64.3 + - - +
1394A TYR 3.2 3.4 + - - -
1395A LEU* 2.8 44.2 + - + +
1396A LEU* 3.1 22.5 + - - +
1433A ILE* 3.8 10.0 - - - +
648H GLN 3.8 13.1 + - - +
649H GLU* 4.5 20.0 - - - +
650H LYS* 5.0 5.4 - - + -
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Residues in contact with MET1393 (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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1392A THR* 1.3 73.5 - - - +
1394A TYR* 1.3 61.1 + - - +
1396A LEU* 3.6 11.3 + - + +
1397A ASP* 3.3 25.1 + - - +
1433A ILE* 3.8 22.4 - - + +
1452A LEU 4.4 19.5 - - - +
1456A THR* 5.5 0.2 - - - +
1457A LEU* 5.5 4.3 - - + -
649H GLU* 3.9 12.6 + - - +
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Residues in contact with TYR1394 (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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1392A THR* 3.2 1.0 + - - -
1393A MET* 1.3 75.9 - - - +
1395A LEU* 1.3 70.0 + - + +
1397A ASP* 3.5 20.0 + - + +
1398A PHE* 3.4 35.9 + + - -
617H LEU* 4.2 19.7 - - + +
647H LYS* 4.1 11.9 - - + -
648H GLN* 3.4 46.7 + - + +
649H GLU* 3.7 17.6 + - + +
70L ARG* 3.4 36.7 + - - -
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Residues in contact with LEU1395 (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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1390A PRO* 3.6 30.1 - - + +
1392A THR* 2.8 35.9 + - + +
1394A TYR* 1.3 87.3 - - + +
1396A LEU* 1.3 59.2 + - - +
1397A ASP 3.0 1.3 - - - -
1398A PHE* 2.8 47.9 + - + +
1399A VAL* 3.4 8.1 + - - +
648H GLN* 4.5 4.7 - - + +
650H LYS* 4.3 27.8 - - + +
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Residues in contact with LEU1396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390A PRO* 3.1 35.6 - - + +
1391A ASP 5.1 1.3 - - - +
1392A THR 3.1 18.2 + - - +
1393A MET* 3.9 12.3 - - - +
1394A TYR 3.5 0.4 - - - -
1395A LEU* 1.3 76.0 - - - +
1397A ASP* 1.3 57.4 + - - +
1399A VAL* 2.9 28.9 + - + +
1404A LEU* 4.1 19.1 - - + -
1431A PRO* 5.3 1.3 - - + -
1433A ILE* 4.8 5.6 - - + -
1434A ILE* 3.8 39.0 - - + -
1456A THR* 4.2 19.7 - - + +
1457A LEU* 4.0 16.8 - - + -
1460A ALA* 4.1 5.6 - - + -
1464A ILE* 5.2 0.7 - - + -
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Residues in contact with ASP1397 (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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1393A MET 3.3 14.1 + - - +
1394A TYR* 3.5 16.2 - - + +
1395A LEU 3.0 1.4 - - - -
1396A LEU* 1.3 73.7 - - - +
1398A PHE* 1.3 63.8 + - - +
1453A ASN* 5.4 5.1 + - - +
1456A THR* 3.9 18.4 + - - +
70L ARG* 3.5 16.7 - - + -
71L LYS* 3.1 52.1 + - + +
133L ARG* 4.0 14.2 + - - -
135L PHE* 3.3 11.6 - - - -
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Residues in contact with PHE1398 (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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1360A VAL* 5.2 7.6 - - - +
1394A TYR* 3.4 42.5 + + - -
1395A LEU* 2.8 34.5 + - + +
1397A ASP* 1.3 73.4 - - - +
1399A VAL* 1.3 64.2 + - + +
1400A LYS 3.6 3.3 + - - -
618H ASP* 5.0 11.7 - - - -
648H GLN* 5.2 4.9 - - - -
69L ARG* 3.4 44.0 - - + +
70L ARG* 3.5 32.2 - - + +
135L PHE* 4.1 2.5 - - - -
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Residues in contact with VAL1399 (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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1390A PRO* 4.7 16.2 - - + -
1395A LEU 4.1 8.3 - - - +
1396A LEU* 2.9 25.7 + - - +
1397A ASP 3.3 0.2 - - - -
1398A PHE* 1.3 82.1 - - + +
1400A LYS* 1.3 77.6 + - - +
1401A PRO* 3.4 3.5 - - - +
1403A PHE* 4.9 2.2 - - + -
1404A LEU* 3.6 33.4 - - + +
1407A ARG* 3.6 35.2 - - - +
1456A THR* 5.6 0.9 - - - +
135L PHE* 3.2 9.5 - - - -
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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