Contacts of the helix formed by residues 1134 - 1152 (chain 3) in PDB entry 6AH0
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 SER1134 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11323 PHE* 3.4 6.1 + - - -
11333 THR* 1.3 81.4 + - - +
11353 HIS* 1.3 63.5 + - - +
11363 GLU 2.9 8.7 + - - +
11373 ASP* 3.8 3.5 + - - +
11383 HIS* 3.4 14.9 + - - -
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Residues in contact with HIS1135 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11343 SER* 1.3 71.6 - - - +
11363 GLU* 1.3 55.8 + - - +
11383 HIS* 3.6 4.3 - - - +
11393 ASP* 2.9 25.8 + - - -
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Residues in contact with GLU1136 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11343 SER* 2.9 7.0 - - - +
11353 HIS* 1.3 75.2 - - - +
11373 ASP* 1.3 67.0 + - - +
11383 HIS 2.9 1.9 + - - -
11403 PHE* 3.0 21.3 + - - -
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Residues in contact with ASP1137 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11343 SER* 3.8 4.9 + - - +
11363 GLU* 1.3 72.4 - - - +
11383 HIS* 1.3 65.4 + - - +
11403 PHE* 4.7 1.3 - - - +
11413 PHE* 2.8 19.6 + - - +
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Residues in contact with HIS1138 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11343 SER 3.4 13.1 + - - -
11353 HIS* 3.5 5.4 - - - +
11363 GLU 2.9 3.2 - - - -
11373 ASP* 1.3 80.2 - - - +
11393 ASP* 1.3 63.3 + - - +
11413 PHE* 3.6 0.7 - - - -
11423 GLN* 2.9 17.3 + - - -
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Residues in contact with ASP1139 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11353 HIS 2.9 17.3 + - - -
11383 HIS* 1.3 70.6 - - - +
11403 PHE* 1.3 66.6 + - - +
11423 GLN* 3.0 5.4 + - - +
11433 HIS* 3.0 14.9 + - - -
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Residues in contact with PHE1140 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11363 GLU 3.0 15.5 + - - -
11373 ASP* 3.8 1.8 - - - +
11393 ASP* 1.3 73.9 - - - +
11413 PHE* 1.3 53.7 + - - +
11433 HIS* 2.6 26.7 + - - -
11443 VAL 2.9 7.8 + - - -
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Residues in contact with PHE1141 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11373 ASP 2.8 18.5 + - - -
11383 HIS 3.6 2.7 - - - -
11403 PHE* 1.3 70.3 - - - +
11423 GLN* 1.3 57.6 + - - +
11443 VAL* 2.5 25.6 + - - +
11453 GLU* 2.9 12.6 + - - -
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Residues in contact with GLN1142 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11383 HIS 2.9 13.6 + - - -
11393 ASP* 3.0 7.1 + - - +
11403 PHE 3.0 0.2 + - - -
11413 PHE* 1.3 74.5 - - - +
11433 HIS* 1.3 61.5 + - - +
11453 GLU* 3.5 1.4 + - - +
11463 MET* 2.9 19.1 + - - -
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Residues in contact with HIS1143 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11393 ASP 3.0 7.0 + - - -
11403 PHE 2.6 14.3 + - - -
11423 GLN* 1.3 69.8 - - - +
11443 VAL* 1.3 68.8 + - - +
11463 MET* 2.9 2.2 + - - +
11473 HIS* 2.9 21.2 + - - +
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Residues in contact with VAL1144 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11403 PHE 2.9 7.8 + - - -
11413 PHE* 2.5 17.7 + - - +
11433 HIS* 1.3 73.0 - - - +
11453 GLU* 1.3 62.1 + - - +
11483 LEU* 2.9 20.4 + - - -
11793 CYS* 6.1 3.1 - - - +
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Residues in contact with GLU1145 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11413 PHE 2.9 11.8 + - - -
11423 GLN 3.9 2.7 - - - -
11443 VAL* 1.3 70.7 - - - +
11463 MET* 1.3 66.0 + - - +
11483 LEU* 3.7 0.4 - - - +
11493 ARG* 2.9 19.2 + - - -
11783 LEU 6.5 0.4 - - - -
11793 CYS* 5.9 5.4 - - - +
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Residues in contact with MET1146 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11423 GLN 2.9 16.0 + - - -
11433 HIS* 2.9 4.6 + - - +
11453 GLU* 1.3 81.0 - - - +
11473 HIS* 1.3 63.4 + - - +
11483 LEU 2.9 0.2 + - - -
11493 ARG* 3.0 9.4 + - - -
11503 SER 4.0 4.5 + - - -
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Residues in contact with HIS1147 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11433 HIS* 2.9 13.9 + - - +
11463 MET* 1.3 71.4 - - - +
11483 LEU* 1.3 65.7 + - - +
11513 GLU* 3.1 17.8 + - - -
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Residues in contact with LEU1148 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11443 VAL 2.9 18.8 + - - -
11453 GLU* 3.7 0.9 - - - +
11463 MET 2.9 0.4 + - - -
11473 HIS* 1.3 74.6 - - - +
11493 ARG* 1.3 52.1 + - - +
11513 GLU* 2.5 9.2 + - - +
11523 HIS* 2.3 40.2 + - - +
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Residues in contact with ARG1149 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11453 GLU 2.9 19.7 + - - -
11463 MET 3.0 3.3 + - - -
11483 LEU* 1.3 72.1 - - - +
11503 SER* 1.3 61.5 + - - +
11523 HIS 2.9 24.7 + - - +
11533 PRO* 3.1 7.7 - - - +
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Residues in contact with SER1150 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11463 MET 4.0 5.3 + - - -
11483 LEU 3.4 0.4 - - - -
11493 ARG* 1.3 73.7 - - - +
11513 GLU* 1.3 58.4 + - - +
11533 PRO* 4.8 2.6 - - - -
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Residues in contact with GLU1151 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11473 HIS 3.1 15.3 + - - -
11483 LEU* 2.5 16.6 + - - -
11503 SER* 1.3 74.1 - - - +
11523 HIS* 1.3 53.5 + - - -
11533 PRO 4.1 0.4 - - - -
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Residues in contact with HIS1152 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11483 LEU* 2.3 23.3 + - - +
11493 ARG* 3.0 9.7 - - - +
11513 GLU* 1.3 71.4 - - - +
11533 PRO* 1.3 68.6 - - - +
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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