Contacts of the helix formed by residues 1238 - 1243 (chain I) in PDB entry 6ALH
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 LEU1238 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690I VAL* 5.6 3.4 - - + -
830I THR* 5.6 0.2 - - + -
832I HIS* 3.6 34.8 - - + +
1058I ARG* 3.7 19.3 - - + -
1064I ASP* 3.3 10.1 - - - +
1234I LYS* 3.4 34.5 - - - +
1235I LEU 3.7 7.2 - - - +
1236I ASN* 3.6 27.2 + - + -
1237I HIS* 1.3 75.8 - - - +
1239I VAL* 1.3 66.8 + - + +
1240I ASP* 3.4 10.8 - - - +
1241I ASP* 3.2 26.0 + - - +
1242I LYS* 3.2 16.4 + - - +
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Residues in contact with VAL1239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061I GLN* 3.7 36.8 - - + +
1062I PRO 4.6 1.1 - - - +
1063I GLY* 4.0 23.1 - - - +
1064I ASP* 2.8 21.7 + - - +
1237I HIS 4.0 0.4 + - - -
1238I LEU* 1.3 72.7 - - - +
1240I ASP* 1.3 60.9 - - - +
1242I LYS* 2.8 9.9 + - + +
1243I MET* 2.7 29.5 + - + +
353J SER* 5.6 1.8 - - - -
354J VAL* 5.3 7.6 - - + -
445J LYS* 3.5 37.9 - - + +
446J ALA* 4.4 3.4 - - + -
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Residues in contact with ASP1240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923I GLY 5.5 2.2 - - - +
924I VAL* 5.5 4.5 - - + +
1058I ARG* 2.5 48.3 + - - +
1061I GLN* 4.4 11.9 + - - +
1238I LEU* 3.7 13.7 - - - +
1239I VAL* 1.3 73.1 + - - +
1241I ASP* 1.3 68.1 + - - +
1243I MET* 4.2 10.2 - - - +
1262I LYS* 3.0 16.3 + - - -
445J LYS* 3.4 34.8 + - + +
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Residues in contact with ASP1241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B C 5.2 7.0 - - - +
19B T 5.4 2.1 + - - +
832I HIS* 4.4 11.5 + - - -
834I GLN* 5.4 2.9 + - - -
1058I ARG* 4.0 16.2 + - - -
1236I ASN 5.5 1.9 - - - +
1238I LEU* 3.2 24.2 + - - +
1239I VAL 3.2 0.8 - - - -
1240I ASP* 1.3 89.4 + - - +
1242I LYS* 1.3 70.5 + - - +
1262I LYS* 2.8 32.4 + - - +
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Residues in contact with LYS1242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B C 5.5 21.0 + - - +
1236I ASN 4.4 1.8 + - - -
1237I HIS* 3.3 49.3 + - - +
1238I LEU 3.4 13.1 + - - +
1239I VAL* 2.8 9.2 + - + +
1241I ASP* 1.3 85.6 - - - +
1243I MET* 1.3 64.8 + - + +
1244I HIS* 3.1 13.3 + - - +
1262I LYS* 5.0 0.2 - - - +
352J ARG* 4.1 10.1 + - - +
353J SER* 5.2 2.0 - - - -
354J VAL* 4.0 29.4 - - + +
465J GLN* 3.4 32.3 - - - +
19R U 6.5 0.2 - - - -
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Residues in contact with MET1243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1239I VAL* 2.7 20.4 + - + +
1240I ASP* 4.2 10.9 - - - +
1241I ASP 3.6 0.4 - - - -
1242I LYS* 1.3 69.6 - - - +
1244I HIS* 1.3 62.5 + - - +
1262I LYS* 4.7 5.2 - - - -
352J ARG 3.8 6.5 - - - -
353J SER* 4.5 4.9 - - - -
369J PRO* 4.2 4.7 - - - -
371J LYS* 4.3 19.7 - - + -
372J MET* 3.6 37.5 - - + +
445J LYS* 3.3 65.3 - - + +
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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