Contacts of the helix formed by residues 6278 - 6289 (chain F) in PDB entry 2H7C
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 THR6278 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482D SIA 3.1 43.7 - - - +
4085D PRO* 4.1 19.1 - - + -
4115D ASP* 2.6 27.2 + - + +
4118D TYR* 4.6 0.2 - - - +
6276F THR 4.2 0.7 - - - -
6277F THR* 1.3 87.8 - - + +
6279F SER* 1.3 64.2 + - - +
6280F ALA 3.5 0.2 + - - -
6281F VAL* 3.1 18.7 + - + +
6282F MET* 3.0 30.2 + - - +
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Residues in contact with SER6279 (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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482D SIA 3.0 17.5 + - - -
6180F THR* 3.6 18.6 + - - -
6182F ASP* 2.7 38.1 + - - -
6184F HIS* 3.7 4.5 - - - -
6262F LYS* 4.7 6.4 - - - +
6278F THR* 1.3 74.2 - - - +
6280F ALA* 1.3 62.9 + - - +
6282F MET* 3.1 18.7 + - - +
6283F VAL* 3.0 30.1 + - - +
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Residues in contact with ALA6280 (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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4058D PRO* 3.7 27.1 - - + -
4060D LEU* 3.7 7.4 - - + +
4115D ASP* 3.2 22.2 - - - +
6184F HIS* 3.9 23.5 - - + +
6278F THR* 3.3 1.0 + - - -
6279F SER* 1.3 78.3 - - - +
6281F VAL* 1.3 57.9 + - - +
6283F VAL* 3.6 3.6 + - - +
6284F HIS* 2.9 31.5 + - - +
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Residues in contact with VAL6281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4060D LEU* 4.6 6.5 - - + -
4113D SER* 3.3 24.9 - - - +
4114D GLU 5.5 0.2 - - - +
4115D ASP* 3.9 9.2 - - + +
6275F LYS* 4.1 30.5 - - + +
6277F THR* 4.3 9.0 - - - +
6278F THR* 3.1 27.9 + - - +
6279F SER 3.2 0.2 - - - -
6280F ALA* 1.3 74.7 - - - +
6282F MET* 1.3 65.8 - - - +
6284F HIS* 3.4 6.1 + - - +
6285F CYS* 3.0 24.6 + - + +
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Residues in contact with MET6282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6178F PHE* 4.8 6.3 - - + -
6180F THR* 4.2 12.6 - - + -
6262F LYS* 4.9 9.4 - - + -
6265F ALA* 4.2 10.3 - - + +
6266F GLU* 3.9 31.9 - - + +
6269F ALA* 4.0 22.2 - - + -
6274F CYS* 4.5 0.6 - - - -
6275F LYS 3.4 22.4 - - - +
6276F THR* 3.7 10.5 - - - +
6278F THR 3.0 15.7 + - - +
6279F SER* 3.1 33.0 + - - +
6281F VAL* 1.3 76.6 - - - +
6283F VAL* 1.3 59.3 + - + +
6285F CYS* 3.6 3.6 - - - +
6286F LEU* 2.9 34.7 + - - +
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Residues in contact with VAL6283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6065F PHE* 4.2 13.0 - - + -
6178F PHE* 4.0 5.8 - - + -
6180F THR* 3.6 24.5 - - + -
6184F HIS* 3.8 16.6 - - + +
6185F SER* 3.6 16.8 - - - -
6279F SER 3.0 18.3 + - - +
6280F ALA* 3.9 4.5 - - - +
6282F MET* 1.3 71.8 - - - +
6284F HIS* 1.3 66.7 + - - +
6286F LEU* 3.3 6.4 + - - +
6287F ARG* 3.0 54.4 + - - +
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Residues in contact with HIS6284 (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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684D SO4 3.3 41.2 + - - -
4060D LEU* 3.8 23.9 - - + +
4061D GLY* 3.5 30.4 + - - -
685F SO4 3.3 33.6 + - - +
6280F ALA 2.9 20.4 + - - +
6281F VAL* 3.8 5.2 - - - +
6283F VAL* 1.3 76.1 - - - +
6285F CYS* 1.3 65.3 + - - +
6287F ARG* 3.3 5.4 + - - +
6288F GLN* 3.0 50.5 + - + +
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Residues in contact with CYS6285 (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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684D SO4 5.9 1.3 - - - +
6273F GLY 4.6 1.6 - - - -
6274F CYS* 2.0 54.1 - - + -
6275F LYS 4.6 3.1 - - - +
6281F VAL* 3.0 18.9 + - + +
6282F MET 3.6 1.8 - - - +
6284F HIS* 1.3 78.2 - - + +
6286F LEU* 1.3 59.0 + - - +
6288F GLN* 2.9 29.5 + - - +
6289F LYS* 3.4 17.5 + - - +
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Residues in contact with LEU6286 (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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6064F ARG* 2.9 21.5 + - - -
6065F PHE* 3.7 19.7 - - + -
6174F ILE* 5.6 1.6 - - + -
6178F PHE* 3.3 47.6 - - + -
6268F ILE* 4.6 9.9 - - + -
6269F ALA* 4.6 11.0 - - + -
6272F ALA* 3.7 30.7 - - + -
6274F CYS* 4.1 7.6 - - - -
6282F MET 2.9 20.3 + - - +
6283F VAL 3.3 2.2 + - - +
6285F CYS* 1.3 76.6 - - - +
6287F ARG* 1.3 58.6 + - - +
6289F LYS* 3.3 11.5 + - + +
6294F LEU* 3.9 20.1 - - + +
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Residues in contact with ARG6287 (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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685F SO4 3.1 43.9 + - - +
6061F GLY* 4.3 14.6 - - - +
6062F PRO* 3.8 10.2 + - - -
6064F ARG* 2.8 38.8 + - + +
6065F PHE* 3.3 29.4 + - + +
6066F THR* 3.3 27.5 - - - +
6184F HIS 4.6 6.1 + - - -
6283F VAL* 3.0 37.9 + - - +
6284F HIS 3.5 7.4 - - - +
6285F CYS 3.1 0.2 - - - -
6286F LEU* 1.3 77.3 - - - +
6288F GLN* 1.3 63.7 + - - +
6289F LYS 3.4 1.3 - - - +
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Residues in contact with GLN6288 (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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684D SO4 5.0 5.4 - - - +
685F SO4 3.3 21.2 + - - -
6284F HIS* 3.0 47.7 + - + +
6285F CYS* 2.9 11.5 + - - +
6287F ARG* 1.3 82.7 + - - +
6289F LYS* 1.3 66.1 + - + +
6290F THR* 3.7 3.8 + - - +
6293F GLU* 4.5 1.0 - - - +
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Residues in contact with LYS6289 (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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584F SO4 3.5 1.9 + - - -
6064F ARG* 2.8 25.8 + - - -
6272F ALA* 3.0 30.3 + - + +
6273F GLY* 4.2 9.7 + - - -
6274F CYS* 3.6 20.6 - - - -
6285F CYS* 3.6 16.0 - - - +
6286F LEU* 3.3 19.4 + - + +
6287F ARG 4.1 0.9 - - - +
6288F GLN* 1.3 81.5 - - + +
6290F THR* 1.3 60.8 + - - +
6293F GLU* 3.2 27.0 + - + +
6294F LEU* 3.9 22.4 - - + -
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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