Contacts of the helix formed by residues 1242 - 1251 (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 GLY1242 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12371 LEU 4.7 0.2 - - - +
12381 ARG* 2.7 28.9 + - - +
12391 VAL* 3.8 4.4 + - - -
12401 ALA 3.2 2.6 + - - -
12411 ILE* 1.3 77.9 - - - +
12431 PRO* 1.3 69.0 - - - +
12441 CYS 3.5 2.0 - - - -
12451 ARG* 4.0 1.4 + - - -
12461 MET* 3.8 7.4 + - - -
11673 TYR 5.6 4.5 - - - -
11683 PHE* 5.9 0.9 - - - -
11693 PRO* 5.4 8.7 - - - -
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Residues in contact with PRO1243 (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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12381 ARG* 4.1 4.3 - - - -
12421 GLY* 1.3 69.9 - - - +
12441 CYS* 1.3 56.9 + - - +
12461 MET* 2.3 35.2 + - - -
12471 LEU* 2.9 10.1 + - - +
11673 TYR 5.4 3.2 - - - -
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Residues in contact with CYS1244 (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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12421 GLY* 3.5 2.2 - - - -
12431 PRO* 1.3 71.1 - - - +
12451 ARG* 1.3 62.3 + - - +
12471 LEU* 3.5 3.0 + - - +
12481 GLN* 3.0 18.4 + - - -
12831 HIS* 5.9 7.0 - - - +
11673 TYR 5.6 3.0 + - - -
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Residues in contact with ARG1245 (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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12411 ILE 5.4 3.3 + - - -
12421 GLY 4.0 3.4 + - - -
12431 PRO 2.6 4.4 + - - -
12441 CYS* 1.3 71.1 - - - +
12461 MET* 1.3 55.3 + - - +
12481 GLN* 2.7 24.7 + - - +
12491 TYR 3.1 6.2 + - - -
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Residues in contact with MET1246 (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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12381 ARG* 6.5 0.7 - - - +
12421 GLY 3.8 6.6 + - - -
12431 PRO* 2.3 18.2 + - - -
12451 ARG* 1.3 65.8 - - - +
12471 LEU* 1.3 52.3 + - - +
12491 TYR* 2.2 31.7 + - - -
12501 CYS* 3.0 6.8 + - - -
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Residues in contact with LEU1247 (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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12431 PRO* 2.9 12.0 + - - +
12441 CYS* 3.8 3.8 - - - +
12461 MET* 1.3 73.6 - - - +
12481 GLN* 1.3 56.7 + - - +
12501 CYS* 2.8 19.6 + - - +
12511 LEU* 3.1 14.0 + - - -
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Residues in contact with GLN1248 (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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12441 CYS 3.0 10.7 + - - -
12451 ARG* 2.7 13.2 + - - +
12471 LEU* 1.3 77.8 - - - +
12491 TYR* 1.3 56.8 + - - -
12511 LEU* 4.6 1.7 + - - +
4962 ASN 5.6 1.1 - - - -
4972 SER* 3.3 14.2 - - - +
4982 VAL* 3.1 25.6 + - - -
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Residues in contact with TYR1249 (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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12451 ARG 3.1 4.6 + - - -
12461 MET* 2.2 24.2 + - - +
12481 GLN 1.3 70.7 - - - +
12501 CYS* 1.3 58.7 + - - +
12511 LEU 3.5 1.3 - - - -
12521 GLN 4.9 2.1 + - - -
12531 GLY* 5.1 2.3 + - - -
4982 VAL* 4.5 12.8 - - - +
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Residues in contact with CYS1250 (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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12461 MET 3.0 5.9 + - - -
12471 LEU* 2.8 10.4 + - - +
12491 TYR* 1.3 80.3 - - - +
12511 LEU* 1.3 67.8 + - - +
12521 GLN 3.6 0.2 - - - -
12531 GLY* 3.6 7.6 + - - +
12541 LEU* 4.0 5.2 + - - -
12651 TYR* 5.3 10.0 - - - +
12691 TYR* 6.4 1.8 - - - +
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Residues in contact with LEU1251 (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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12471 LEU 3.1 11.7 + - - -
12481 GLN 4.6 1.8 + - - -
12491 TYR 3.5 1.8 - - - -
12501 CYS* 1.3 77.6 - - - +
12521 GLN* 1.3 55.3 + - - +
12531 GLY 2.7 13.4 + - - -
12541 LEU* 2.9 11.4 + - - -
12551 PHE 4.8 0.3 + - - -
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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