Contacts of the helix formed by residues 345 - 349 (chain B) in PDB entry 1A7A
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 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B LEU* 3.7 30.5 - - + +
202B GLY* 4.0 10.6 - - - -
203B ILE 4.4 1.1 - - - +
297B CYS* 3.9 15.0 - - + -
298B ASN 2.8 20.6 + - - +
299B ILE* 4.3 4.5 - - + +
339B LEU* 4.0 25.6 - - + +
340B ALA* 4.6 2.5 - - - -
343B ARG 2.8 9.0 + - - +
344B LEU* 1.3 70.2 - - - +
346B ASN* 1.3 66.0 + - - +
348B GLY 4.3 0.9 - - - +
349B CYS* 2.7 54.5 + - + +
350B ALA 3.7 0.5 + - - -
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Residues in contact with ASN 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 3.4 48.5 + - - +
199B LEU 4.2 0.2 - - - +
202B GLY* 4.6 2.7 - - - -
299B ILE* 3.9 10.8 - - + +
344B LEU* 3.6 13.1 + - - +
345B VAL* 1.3 79.0 - - - +
347B LEU* 1.3 76.0 + - - +
350B ALA* 3.0 20.4 + - - +
352B GLY* 3.0 19.3 + - - -
353B HIS* 3.9 3.5 + - - -
434B NAD 2.7 42.7 + - - +
436B ADC 4.3 3.3 - - - -
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B HIS* 3.1 45.1 - - + +
57B THR* 4.1 21.1 - - + -
82B PHE 3.9 2.9 - - - +
83B SER* 3.5 21.8 - - - +
85B GLN* 6.1 0.5 - - - +
103B LYS* 3.7 8.0 + - - -
344B LEU* 3.5 17.5 - - + +
346B ASN* 1.3 87.6 - - - +
348B GLY* 1.3 64.7 + - - +
350B ALA 3.4 13.7 - - - +
351B MSE 4.3 1.1 - - - +
352B GLY* 3.4 25.4 - - - +
436B ADC 3.8 26.5 - - + +
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Residues in contact with GLY 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 5.9 0.2 - - - -
82B PHE* 4.0 23.3 - - - -
83B SER* 4.7 0.8 - - - +
103B LYS* 2.8 25.6 + - - -
324B GLN* 3.9 12.1 - - - +
340B ALA* 4.3 8.5 - - - -
343B ARG 5.8 0.4 - - - -
344B LEU* 3.0 17.2 + - - +
347B LEU* 1.3 78.8 - - - +
349B CYS* 1.3 60.9 + - - +
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Residues in contact with CYS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS* 5.5 0.4 - - - -
202B GLY* 3.4 17.7 - - - +
205B ARG* 3.5 21.7 - - - +
206B ALA* 3.9 16.1 + - + -
324B GLN* 3.8 28.7 - - - -
325B VAL* 5.1 0.2 - - - -
339B LEU* 4.0 2.0 - - - -
340B ALA* 3.9 14.4 - - - -
345B VAL* 2.7 35.2 + - + +
348B GLY* 1.3 75.1 - - - -
350B ALA* 1.3 60.9 + - - +
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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