Contacts of the helix formed by residues 505 - 513 (chain F) 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 GLY 505 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501F GLU 3.9 3.8 + - - -
502F MET 3.6 6.6 + - - -
504F ARG* 1.3 78.5 - - - +
506F ILE* 1.3 62.0 + - - +
507F LYS* 3.1 4.9 - - - -
508F LEU* 3.0 23.8 + - - +
509F LEU* 3.3 9.3 - - - +
1429F VAL* 3.8 31.2 - - - +
1431F PHE* 6.5 0.2 - - - -
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Residues in contact with ILE 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502F MET* 3.3 15.6 + - + +
503F LEU* 3.7 35.2 - - + +
504F ARG 3.3 4.3 + - - +
505F GLY* 1.3 76.5 - - - +
507F LYS* 1.3 60.2 + - + +
509F LEU* 3.2 17.0 + - + +
510F LYS* 2.9 29.7 + - + +
515F GLU* 3.8 18.2 - - + +
1105F ILE* 5.3 5.8 - - + +
1109F MET* 4.7 4.7 - - + -
1112F PHE* 3.7 53.8 - - + -
1117F LEU* 5.2 2.0 - - + -
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Residues in contact with LYS 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505F GLY* 3.1 1.5 - - - -
506F ILE* 1.3 79.9 - - + +
508F LEU* 1.3 65.0 + - - +
510F LYS* 3.2 1.4 + - - +
511F LEU* 2.9 42.7 + - + +
1109F MET* 3.5 28.7 - - + -
1389F LEU* 5.2 12.7 - - + +
1394F MET* 4.1 16.4 - - + -
1425F LEU* 3.7 40.2 - - + +
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Residues in contact with LEU 508 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505F GLY* 3.0 14.8 + - - +
507F LYS* 1.3 79.5 - - - +
509F LEU* 1.3 59.8 + - + +
511F LEU* 3.1 5.3 + - - -
512F TYR* 2.9 64.3 + - + +
514F TRP* 4.2 12.3 - - + -
1425F LEU* 5.7 8.7 - - + +
1429F VAL* 3.6 32.8 - - + +
1431F PHE* 3.3 35.2 - - + -
1493F ARG* 3.2 24.0 - - - +
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Residues in contact with LEU 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501F GLU 5.5 0.4 - - - +
502F MET* 3.6 41.3 - - + +
505F GLY 3.3 17.3 - - - +
506F ILE* 3.2 9.7 + - + +
508F LEU* 1.3 79.1 - - - +
510F LYS* 1.3 65.4 + - - +
512F TYR 4.6 0.2 - - - +
513F ALA* 3.1 25.3 + - - -
514F TRP* 3.6 5.7 + - - +
515F GLU* 3.1 32.9 - - + +
518F PHE* 3.4 33.2 - - + -
1105F ILE* 6.2 0.2 - - + -
1431F PHE* 3.9 28.7 - - + -
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Residues in contact with LYS 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506F ILE* 2.9 20.2 + - + +
507F LYS 3.2 4.7 + - - +
509F LEU* 1.3 76.4 - - - +
511F LEU* 1.3 55.5 + - - +
513F ALA* 4.2 3.5 + - - +
515F GLU* 2.8 32.7 + - - +
1105F ILE 3.9 6.1 + - - +
1106F LEU 4.4 0.2 + - - -
1107F ALA 3.3 26.1 + - - +
1108F PRO* 4.4 9.8 - - - +
1109F MET* 3.5 27.6 - - + +
1112F PHE* 4.9 4.7 - - + -
1323F GLU* 5.1 0.8 - - - +
1325F TYR* 3.3 32.5 + - - -
1394F MET* 4.8 1.8 - - - -
1418F ARG* 2.6 39.3 + - - +
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Residues in contact with LEU 511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507F LYS* 2.9 43.8 + - + +
508F LEU* 3.6 6.7 - - - +
509F LEU 3.0 0.2 - - - -
510F LYS* 1.3 77.2 - - - +
512F TYR* 1.3 67.8 + - + +
513F ALA 3.3 0.4 - - - -
1389F LEU* 4.1 13.9 - - + -
1392F PHE* 3.4 32.3 - - + -
1394F MET* 3.7 32.1 - - + -
1418F ARG* 3.1 31.7 - - - +
1423F ILE* 4.2 23.6 - - + -
1425F LEU* 5.2 12.1 - - + -
1497F ARG* 5.1 0.5 + - - -
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Residues in contact with TYR 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508F LEU* 2.9 60.4 + - + +
509F LEU 4.7 0.2 - - - +
511F LEU* 1.3 78.7 - - + +
513F ALA* 1.3 71.3 + - - +
514F TRP* 3.2 31.3 - + + +
1418F ARG 4.5 1.2 - - - +
1419F SER* 5.2 1.2 - - - -
1422F SER* 5.4 1.6 - - - -
1423F ILE* 2.5 40.4 + - + +
1424F ILE* 4.2 5.2 - - - -
1425F LEU* 4.6 6.7 + - + +
1490F CYS* 4.7 2.9 + - - +
1493F ARG* 3.9 23.1 + - + -
1494F ALA* 4.4 20.1 - - + +
1497F ARG* 2.8 52.2 + - - +
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Residues in contact with ALA 513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F LEU 3.1 10.7 + - - -
510F LYS 4.2 3.1 + - - +
511F LEU 3.3 3.0 - - - -
512F TYR* 1.3 80.8 - - - +
514F TRP* 1.3 66.8 + - - +
515F GLU* 3.5 4.5 - - - +
516F ASN* 5.4 1.7 + - - +
517F ILE* 4.4 4.9 - - - +
1415F HIS* 4.1 33.6 + - + +
1418F ARG* 4.5 6.3 - - + -
1419F SER* 3.9 28.7 - - - +
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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