Contacts of the helix formed by residues 339 - 346 (chain A) in PDB entry 1W88
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 LYS 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A PRO* 6.6 0.2 - - - -
337A LYS* 4.5 8.1 - - + +
338A GLN* 1.3 77.9 - - - +
340A VAL* 1.3 66.2 + - - +
341A THR* 3.8 8.1 - - - +
342A ASP* 3.0 36.0 + - - +
343A LEU* 3.4 12.6 + - - +
366A GLU* 3.5 37.7 - - + +
306D VAL* 4.9 3.1 - - - -
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LYS* 1.3 71.0 - - - +
341A THR* 1.3 63.9 + - - +
343A LEU* 2.9 20.6 + - + +
344A ILE* 3.0 20.8 + - + +
362A TYR* 3.6 39.5 - - + -
366A GLU* 3.5 5.5 + - - +
294D PRO* 3.7 22.7 - - + -
306D VAL* 3.5 42.9 - - + +
307D TRP* 4.1 13.7 - - + -
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Residues in contact with THR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LYS* 3.8 7.8 - - - +
340A VAL* 1.3 74.4 - - - +
342A ASP* 1.3 60.8 + - - +
344A ILE* 3.2 8.9 + - - +
345A SER* 2.8 33.8 + - - -
359A TYR* 3.7 38.9 - - + +
362A TYR* 3.9 3.8 - - + -
363A LYS* 3.6 28.0 - - + +
366A GLU* 2.6 34.8 + - - +
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Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.0 28.2 - - + -
337A LYS 4.2 3.1 - - - +
338A GLN* 3.9 5.4 - - - -
339A LYS* 3.0 42.2 + - - +
341A THR* 1.3 80.2 + - - +
343A LEU* 1.3 65.1 + - + +
345A SER* 3.3 8.5 + - - -
346A ILE* 3.2 28.8 + - - +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.6 5.6 - - + -
338A GLN* 3.9 22.0 - - + +
339A LYS 3.5 13.7 - - - +
340A VAL* 2.9 12.0 + - + +
342A ASP* 1.3 75.2 - - - +
344A ILE* 1.3 64.1 + - - +
346A ILE* 3.2 23.9 + - + +
347A MET* 3.5 12.1 - - - +
102B TYR* 3.8 31.9 - - + +
296D THR* 4.1 11.2 - - + +
299D PRO* 4.1 7.9 - - + -
300D PHE* 4.4 3.4 - - + -
303D ALA* 3.9 24.9 - - + -
307D TRP* 3.8 26.9 - - + -
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A VAL* 3.0 33.9 + - + +
341A THR* 3.6 8.7 - - - +
343A LEU* 1.3 76.1 - - - +
345A SER* 1.3 62.7 + - - +
347A MET* 3.1 16.9 + - - +
351A LEU* 3.4 16.8 - - + +
355A LEU* 3.6 35.9 - - + +
358A GLN* 3.8 18.4 - - + +
359A TYR* 3.7 37.2 - - + +
362A TYR* 4.4 1.6 - - + -
294D PRO* 4.9 2.9 - - + -
296D THR* 3.7 23.3 - - + -
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A THR 2.8 23.3 + - - -
342A ASP* 3.3 9.5 + - - -
344A ILE* 1.3 74.2 - - - +
346A ILE* 1.3 62.1 + - - +
348A PHE 3.4 18.9 - - - +
351A LEU* 4.4 8.7 - - - +
359A TYR* 3.2 22.7 + - - -
101B ARG* 5.5 0.2 - - - -
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Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.1 30.3 - - + -
130A GLN* 5.2 3.8 - - - +
342A ASP 3.2 13.0 - - - +
343A LEU* 3.2 18.6 - - + +
345A SER* 1.3 79.8 - - - +
347A MET* 1.3 61.0 + - - +
348A PHE 3.7 0.2 - - - -
101B ARG* 3.2 13.2 - - - +
102B TYR* 3.0 62.0 + - + +
105B GLY* 4.0 26.7 - - - +
106B GLY* 4.4 2.2 - - - +
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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