Contacts of the helix formed by residues 727 - 737 (chain 1) 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 VAL 727 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6911 GLU* 6.3 2.9 - - - +
7241 PHE 2.8 13.6 + - - -
7251 ASP 2.7 5.9 + - - -
7261 SER* 1.3 74.8 - - - +
7281 LEU* 1.3 66.9 + - - +
7291 LYS 3.3 0.5 + - - -
7301 PRO* 3.6 6.4 - - - +
7311 LEU* 3.7 4.7 + - - -
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Residues in contact with LEU 728 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7241 PHE 3.8 2.8 + - - -
7251 ASP 2.9 11.7 + - - -
7271 VAL* 1.3 72.6 - - - +
7291 LYS* 1.3 52.7 + - - +
7301 PRO 2.6 0.9 - - - -
7311 LEU* 2.1 43.0 + - - +
7321 TRP 3.3 3.7 + - - +
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Residues in contact with LYS 729 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7251 ASP 4.7 1.4 + - - -
7261 SER 4.5 3.2 + - - -
7271 VAL 3.3 1.4 + - - -
7281 LEU* 1.3 72.1 - - - +
7301 PRO* 1.3 62.6 - - - +
7321 TRP* 3.9 2.7 + - - +
7331 LYS* 3.5 14.2 + - - -
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Residues in contact with PRO 730 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7261 SER 5.3 1.2 - - - -
7271 VAL 3.6 5.0 - - - +
7281 LEU 2.6 5.4 - - - -
7291 LYS* 1.3 71.5 - - - +
7311 LEU* 1.3 53.8 + - - +
7331 LYS* 3.0 3.7 + - - -
7341 GLY* 2.6 34.1 + - - -
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Residues in contact with LEU 731 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7271 VAL 3.7 5.3 + - - -
7281 LEU* 2.1 22.0 + - - +
7301 PRO* 1.3 66.2 - - - +
7321 TRP* 1.3 63.9 + - - +
7341 GLY* 2.9 4.4 + - - -
7351 ILE* 2.8 21.5 + - - -
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Residues in contact with TRP 732 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7281 LEU* 3.3 8.1 + - - +
7291 LYS* 3.9 2.8 + - - +
7301 PRO 3.3 0.6 - - - -
7311 LEU* 1.3 74.3 - - - +
7331 LYS* 1.3 65.0 + - - +
7351 ILE* 2.9 13.1 + - - +
7361 ARG 3.6 2.9 + - - -
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Residues in contact with LYS 733 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7291 LYS 3.5 10.7 + - - -
7301 PRO* 3.0 6.7 + - - -
7321 TRP* 1.3 74.9 - - - +
7341 GLY* 1.3 63.6 + - - +
7361 ARG* 2.9 16.5 + - - -
7371 GLN 3.8 2.6 + - - -
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Residues in contact with GLY 734 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7301 PRO 2.6 17.8 + - - -
7311 LEU* 3.3 4.5 - - - -
7331 LYS* 1.3 69.8 - - - +
7351 ILE* 1.3 64.4 + - - +
7361 ARG 3.0 1.2 + - - -
7371 GLN* 3.1 12.0 + - - -
7381 HIS* 3.9 6.9 + - - -
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Residues in contact with ILE 735 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7311 LEU 2.8 16.0 + - - -
7321 TRP* 2.9 6.7 + - - +
7341 GLY* 1.3 73.5 - - - +
7361 ARG* 1.3 64.4 + - - +
7381 HIS* 3.8 6.6 + - - +
7431 LEU* 6.0 5.5 - - - +
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Residues in contact with ARG 736 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7321 TRP 3.6 4.2 + - - -
7331 LYS 2.9 10.9 + - - -
7351 ILE* 1.3 77.9 - - - +
7371 GLN* 1.3 57.3 + - - +
7381 HIS 3.2 7.0 + - - +
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Residues in contact with GLN 737 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7331 LYS 3.8 4.0 + - - -
7341 GLY 3.1 7.9 + - - -
7361 ARG* 1.3 75.4 - - - +
7381 HIS* 1.3 61.0 + - - +
7391 ARG 4.0 0.5 + - - -
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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