Contacts of the helix formed by residues 5002 - 5014 (chain F) in PDB entry 6X34
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 THR5002 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3890F HIS* 3.8 1.9 - - - -
3965F GLN* 3.2 15.7 + - - +
4023F LEU 5.7 0.3 - - - -
4024F SER* 4.4 16.2 - - - -
4027F GLU* 5.0 4.9 - - - +
4188F ILE* 5.4 7.2 - - + -
4992F TYR* 6.1 1.5 - - + -
5001F HIS* 1.3 76.3 - - - +
5003F GLY* 1.3 65.7 + - - +
5004F GLN* 3.6 9.3 + - + +
5005F GLU* 3.4 24.3 - - + +
5006F SER* 3.0 30.1 + - - -
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Residues in contact with GLY5003 (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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3890F HIS* 4.8 3.4 - - - -
3965F GLN 3.2 24.6 + - - -
3966F GLY* 3.9 13.7 - - - -
3967F PRO* 4.6 11.8 - - - +
4027F GLU* 5.4 5.8 - - - +
5002F THR* 1.3 83.4 + - - +
5004F GLN* 1.3 57.2 + - - -
5006F SER* 4.5 1.3 - - - -
5007F TYR* 3.6 20.3 + - - +
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Residues in contact with GLN5004 (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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4027F GLU* 5.3 10.0 - - + +
4178F ILE* 5.0 12.8 - - + +
4188F ILE* 4.1 30.5 - - + -
4989F PHE* 5.9 1.3 - - - -
5002F THR* 3.2 9.5 + - + +
5003F GLY* 1.3 79.6 - - - +
5005F GLU* 1.3 63.5 + - - +
5006F SER 3.3 0.2 - - - -
5007F TYR* 3.4 6.1 + - - +
5008F VAL* 3.3 24.1 + - - +
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Residues in contact with GLU5005 (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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4188F ILE* 5.7 2.1 - - + +
4989F PHE* 5.2 4.9 - - + -
4992F TYR* 4.8 11.2 - - + -
4993F LEU* 3.4 20.5 - - + +
5001F HIS* 3.8 11.9 - - + -
5002F THR* 3.4 29.7 - - + +
5004F GLN* 1.3 78.4 - - - +
5006F SER* 1.3 58.0 + - - +
5008F VAL* 3.3 10.8 - - - +
5009F TRP* 3.2 27.7 + - - +
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Residues in contact with SER5006 (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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3890F HIS* 3.5 25.4 - - - -
4998F GLU 5.9 0.4 - - - -
5001F HIS* 4.1 8.2 - - - +
5002F THR 3.0 19.0 + - - -
5003F GLY* 4.5 2.9 - - - -
5005F GLU* 1.3 74.3 - - - +
5007F TYR* 1.3 60.3 + - - +
5009F TRP* 3.8 7.2 - - - +
5010F LYS* 3.0 28.6 + - - +
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Residues in contact with TYR5007 (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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3967F PRO* 6.2 4.0 - - + -
4178F ILE* 4.2 19.3 - - + -
4179F MET 5.0 1.1 - - - -
4180F GLY* 3.3 23.7 - - - -
4181F ALA* 3.3 27.0 + - + +
5003F GLY 3.6 17.0 + - - +
5004F GLN* 3.4 8.0 + - - +
5005F GLU 3.3 0.6 - - - -
5006F SER* 1.3 77.2 - - - +
5008F VAL* 1.3 67.5 + - - +
5010F LYS* 3.4 6.9 + - + +
5011F MET* 3.2 26.8 + - + +
5019F PHE* 6.4 3.6 - - + -
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Residues in contact with VAL5008 (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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4178F ILE* 4.7 10.1 - - + -
4989F PHE* 3.8 38.8 - - + -
4993F LEU* 4.7 5.8 - - + -
5004F GLN 3.3 12.9 + - - +
5005F GLU* 3.3 15.5 - - - +
5007F TYR* 1.3 81.4 - - + +
5009F TRP* 1.3 62.6 + - - +
5011F MET* 3.4 5.5 + - - +
5012F TYR* 2.9 29.8 + - + +
5019F PHE* 3.8 38.5 - - + +
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Residues in contact with TRP5009 (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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3748F PHE* 5.6 12.8 - + - -
4993F LEU* 3.7 42.4 - - + -
4994F ILE* 3.7 32.3 - - + -
4998F GLU* 5.2 16.0 - - + +
5005F GLU 3.2 19.9 + - - +
5006F SER* 3.9 7.2 - - - +
5007F TYR 3.3 0.2 - - - -
5008F VAL* 1.3 76.7 - - - +
5010F LYS* 1.3 65.9 + - - +
5012F TYR* 3.4 32.7 + + + +
5013F GLN* 3.4 17.6 + - + +
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Residues in contact with LYS5010 (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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5006F SER 3.0 19.3 + - - +
5007F TYR* 3.7 8.7 - - + +
5008F VAL 3.3 0.2 - - - -
5009F TRP* 1.3 81.4 - - - +
5011F MET* 1.3 60.3 + - - +
5012F TYR 3.6 0.2 + - - -
5013F GLN* 3.7 5.5 + - - +
5014F GLU* 3.7 16.5 + - - +
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Residues in contact with MET5011 (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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5007F TYR* 3.2 20.8 + - + +
5008F VAL* 3.4 6.5 + - - +
5010F LYS* 1.3 76.4 - - - +
5012F TYR* 1.3 64.3 + - - +
5014F GLU* 3.3 16.4 + - - +
5016F CYS* 2.8 32.9 - - + +
5018F ASP 5.9 0.7 - - - +
5019F PHE* 5.2 14.4 - - + +
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Residues in contact with TYR5012 (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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4230F VAL* 3.6 29.9 + - + +
4234F GLU* 5.3 5.2 - - - +
4714F TRP* 4.4 19.1 - + - -
4990F LEU* 4.2 21.0 - - + +
4994F ILE* 5.5 6.3 - - + -
5008F VAL* 2.9 20.8 + - + +
5009F TRP* 3.7 34.1 - + + +
5010F LYS 3.3 0.2 - - - -
5011F MET* 1.3 77.8 - - - +
5013F GLN* 1.3 64.0 + - + +
5014F GLU 3.4 7.4 - - - +
5016F CYS 4.8 1.6 - - - -
5017F TRP* 4.2 25.6 + + - +
5019F PHE* 4.9 11.0 - + + -
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Residues in contact with GLN5013 (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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5009F TRP* 3.4 18.0 + - + +
5010F LYS* 4.1 5.6 - - - +
5011F MET 3.3 0.6 - - - -
5012F TYR* 1.3 83.3 - - + +
5014F GLU* 1.3 60.8 + - - +
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Residues in contact with GLU5014 (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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5010F LYS 3.7 11.4 + - - +
5011F MET* 3.3 14.2 + - - +
5012F TYR 3.2 10.8 - - - +
5013F GLN* 1.3 83.3 - - - +
5015F ARG* 1.3 60.1 + - - +
5016F CYS* 3.2 14.5 + - + +
5017F TRP* 3.9 10.2 - - - -
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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