Contacts of the helix formed by residues 1434 - 1440 (chain H) in PDB entry 6C3P
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 THR1434 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1433H GLY* 1.3 72.4 - - - -
1435H ILE* 1.3 60.6 + - - +
1436H ARG* 3.8 13.7 - - + -
1437H PHE* 2.8 24.3 + - + +
1438H ASN* 2.4 42.3 + - - +
1470H LEU 3.2 2.1 + - - -
1471H ASP* 3.0 26.2 - - - +
1472H ALA 3.0 19.9 + - - -
1473H ILE* 5.7 1.6 - - - -
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Residues in contact with ILE1435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434H THR* 1.3 79.8 + - - +
1436H ARG* 1.3 59.9 + - - +
1438H ASN* 3.8 5.4 - - + +
1439H LEU* 2.9 48.6 + - + +
1450H LEU* 5.8 0.4 - - + -
1454H LEU* 4.7 10.8 - - + -
1463H VAL* 5.8 4.0 - - + -
1466H LEU* 6.5 2.2 - - + -
1470H LEU* 3.2 50.0 - - + +
1471H ASP 4.6 0.2 - - - +
1472H ALA* 5.1 7.4 - - + +
1474H ILE* 4.0 28.0 - - + -
1481H PHE* 6.0 0.9 - - + -
1489H PHE* 4.1 23.1 - - + -
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Residues in contact with ARG1436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434H THR* 3.8 11.0 - - + -
1435H ILE* 1.3 76.4 - - - +
1437H PHE* 1.3 58.1 + - - +
1440H ASP* 2.7 37.9 + - - +
1447H ASP* 2.7 43.2 + - - -
1450H LEU* 3.8 13.0 - - - -
1469H GLY 5.3 0.6 + - - -
1470H LEU* 3.2 21.6 + - + +
1471H ASP* 3.9 24.3 + - - +
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Residues in contact with PHE1437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501H GLU* 5.9 1.1 - - - -
517H ILE* 5.8 1.3 - - + -
518H PHE* 3.5 32.9 - + - -
521H ARG* 3.3 53.6 - - - -
1431H PHE* 4.3 20.1 - + + +
1432H SER 4.1 18.2 - - - -
1433H GLY* 4.4 6.1 - - - -
1434H THR* 2.8 24.5 + - + +
1436H ARG* 1.3 74.9 - - - +
1438H ASN* 1.3 65.3 + - - +
1439H LEU 3.5 0.2 + - - -
1440H ASP 3.5 21.3 - - - +
1441H PRO* 3.9 14.8 - - + +
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Residues in contact with ASN1438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514H TRP* 4.6 3.1 - - - -
1430H LEU* 5.1 1.1 - - + +
1431H PHE* 2.3 59.2 + - + +
1433H GLY* 3.6 4.2 - - - +
1434H THR* 2.4 49.3 + - - +
1435H ILE* 3.5 8.4 + - + +
1437H PHE* 1.3 72.4 - - - +
1439H LEU* 1.3 63.9 + - + +
1474H ILE* 3.1 28.0 - - + +
1489H PHE* 6.5 0.2 - - + -
1493H ARG* 3.4 23.0 + - - +
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Residues in contact with LEU1439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514H TRP* 3.9 11.3 - - - -
1435H ILE* 2.9 38.1 + - + +
1438H ASN* 1.3 81.2 - - + +
1440H ASP* 1.3 66.8 + - - +
1441H PRO* 3.1 12.6 - - - +
1450H LEU* 3.9 32.3 - - + +
1453H ALA* 5.5 1.8 - - + -
1454H LEU* 4.7 13.5 - - + -
1489H PHE* 4.3 10.1 - - + +
1492H ALA* 4.2 6.1 - - + -
1493H ARG* 3.5 40.3 - - + +
1496H VAL* 4.0 19.3 - - + +
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Residues in contact with ASP1440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1436H ARG* 2.7 28.3 + - - +
1437H PHE* 3.5 12.0 - - - -
1439H LEU* 1.3 75.7 - - - +
1441H PRO* 1.3 63.5 - - - +
1442H GLU 2.9 22.1 - - - +
1443H ARG* 4.8 2.9 - - - -
1445H CYS* 3.2 39.0 + - - +
1450H LEU* 3.2 31.6 - - - +
1496H VAL* 3.8 11.4 - - - +
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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