Contacts of the helix formed by residues 1434 - 1446 (chain H) in PDB entry 1P3F
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 TYR1434 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025G PHE* 4.1 21.5 - + + -
1026G PRO* 4.7 12.3 - - + -
1029G ARG* 4.5 20.2 - - - -
1030G VAL* 4.8 8.8 - - + +
1033G LEU* 3.5 25.1 - - + +
1055G LEU* 4.6 1.9 - - + +
1433H SER* 1.3 77.1 + - - +
1435H ALA* 1.3 54.3 + - - +
1436H ILE 3.1 2.9 - - - -
1437H TYR* 2.5 36.3 + + + -
1438H VAL* 2.8 23.7 + - + -
1460H ASN* 3.1 26.3 + - - +
1463H VAL* 3.5 40.6 - - + +
1464H ASN* 3.1 25.8 + - - -
1467H PHE* 4.2 17.2 - - - +
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Residues in contact with ALA1435 (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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1433H SER* 2.7 16.0 + - - +
1434H TYR* 1.3 77.6 - - - +
1436H ILE* 1.3 64.6 + - + +
1437H TYR 3.1 0.7 + - - -
1438H VAL* 3.6 1.6 - - - +
1439H TYR* 3.1 23.4 + - - +
1456H MET* 3.6 39.2 - - + +
1460H ASN* 4.6 2.7 + - + -
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Residues in contact with ILE1436 (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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1433H SER 4.6 1.0 + - - +
1434H TYR 2.9 0.2 + - - -
1435H ALA* 1.3 80.8 - - + +
1437H TYR* 1.3 87.3 + - + +
1439H TYR* 4.0 5.7 + - - +
1440H LYS* 3.1 35.3 + - + +
121I G 3.5 48.9 - - + +
122I G 3.8 13.1 + - - +
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Residues in contact with TYR1437 (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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1024G GLN 3.1 24.7 - - - +
1025G PHE* 3.8 23.3 - - + -
1026G PRO* 3.0 40.6 - - + +
1029G ARG* 4.1 12.7 + - - -
1433H SER 4.3 10.5 - - - -
1434H TYR* 2.5 28.3 + + + +
1436H ILE* 1.3 97.9 - - + +
1438H VAL* 1.3 67.4 + - - +
1440H LYS* 2.9 22.3 + - + +
1441H VAL* 2.9 19.6 + - - +
121I G 3.4 34.7 + - - -
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Residues in contact with VAL1438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025G PHE* 4.6 4.0 - - + -
1059G THR* 4.5 11.9 - - + -
1063G LEU* 3.7 20.4 - - + +
1434H TYR* 2.8 28.2 + - + +
1435H ALA* 3.6 4.9 - - - +
1437H TYR* 1.3 79.1 - - - +
1439H TYR* 1.3 54.0 + - - +
1441H VAL* 3.1 6.7 + - - +
1442H LEU* 2.6 34.5 + - + +
1451H ILE* 4.9 1.3 - - + -
1456H MET* 3.7 25.6 - - + -
1459H MET* 4.1 27.6 - - + -
1460H ASN 5.2 0.7 - - - +
1463H VAL* 5.1 5.4 - - + -
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Residues in contact with TYR1439 (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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1435H ALA 3.1 13.7 + - - +
1436H ILE* 4.1 5.2 - - - +
1438H VAL* 1.3 80.4 - - - +
1440H LYS* 1.3 72.5 + - + +
1442H LEU* 2.9 28.7 + - + +
1443H LYS* 3.0 53.2 + - + +
1450H GLY* 5.2 1.6 - - - -
1451H ILE* 4.1 14.4 - - + -
1456H MET* 4.0 9.4 - - + +
166J T 4.4 26.1 + - - -
167J T 5.2 7.0 + - - -
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Residues in contact with LYS1440 (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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1024G GLN* 3.7 36.1 + - + +
1436H ILE* 3.1 26.2 + - - +
1437H TYR* 2.9 17.8 + - + +
1439H TYR* 1.3 84.8 - - + +
1441H VAL* 1.3 63.5 + - - +
1443H LYS* 3.1 5.8 + - - +
1444H GLN* 3.1 20.8 + - - +
121I G 4.8 12.5 + - - -
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Residues in contact with VAL1441 (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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1024G GLN* 3.9 14.4 - - + -
1025G PHE* 3.4 29.2 - - + -
1056G GLU* 4.0 11.7 - - + +
1059G THR* 4.1 15.5 - - + -
1060G ALA* 4.0 29.4 - - + +
1063G LEU* 4.3 0.7 - - + -
1437H TYR 2.9 17.8 + - - +
1438H VAL 3.4 5.4 - - - +
1440H LYS* 1.3 70.9 - - - +
1442H LEU* 1.3 66.2 + - - +
1444H GLN* 3.2 24.3 + - + +
1445H VAL* 3.3 11.7 + - + +
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Residues in contact with LEU1442 (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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1063G LEU* 3.6 36.0 - - + +
1078G ILE* 4.4 12.6 - - + -
1438H VAL* 2.6 17.5 + - + +
1439H TYR* 2.9 24.6 + - + +
1441H VAL* 1.3 72.8 - - - +
1443H LYS* 1.4 54.0 + - + +
1445H VAL* 2.8 8.6 + - - +
1446H HIS* 2.7 53.1 + - + +
1449H THR* 3.6 23.6 - - - +
1450H GLY 4.3 1.3 - - - -
1451H ILE* 3.7 34.1 - - + -
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Residues in contact with LYS1443 (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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1439H TYR* 3.0 54.4 + - + +
1440H LYS* 3.6 8.5 - - - +
1442H LEU* 1.4 75.9 - - + +
1444H GLN* 1.3 56.9 + - - +
1445H VAL 3.0 5.2 - - - -
1446H HIS 4.0 0.7 - - - +
1447H PRO* 3.0 60.0 + - + +
1448H ASP 4.1 1.8 - - - -
1449H THR 2.3 38.6 + - - +
1450H GLY* 4.2 2.6 - - - -
166J T 5.8 0.2 + - - -
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Residues in contact with GLN1444 (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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1024G GLN* 3.6 30.8 + - - +
1056G GLU* 4.6 5.4 + - - +
1440H LYS 3.1 11.0 + - - +
1441H VAL* 3.2 16.1 + - + +
1443H LYS* 1.3 76.8 - - - +
1445H VAL* 1.3 61.9 + - + +
1447H PRO* 4.9 2.6 - - - +
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Residues in contact with VAL1445 (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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1060G ALA* 4.3 27.6 - - + +
1063G LEU* 4.6 2.0 - - + -
1064G GLU* 3.5 39.1 - - + +
1441H VAL* 3.3 11.9 + - + +
1442H LEU* 2.8 12.6 + - - +
1444H GLN* 1.3 85.5 - - + +
1446H HIS* 1.3 84.1 + - + +
1447H PRO* 3.7 7.2 - - - +
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Residues in contact with HIS1446 (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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1063G LEU 3.5 11.9 - - - -
1064G GLU* 3.0 33.7 + - - -
1067G GLY* 3.4 23.6 - - - -
1068G ASN* 3.5 20.6 - - - -
1442H LEU* 2.7 22.7 + - + +
1443H LYS* 4.0 1.6 - - - +
1445H VAL* 1.3 90.4 + - + +
1447H PRO* 1.3 62.4 - - - +
1448H ASP 3.1 2.7 - - - -
1449H THR* 2.8 45.6 + - - +
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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