Contacts of the strand formed by residues 341 - 348 (chain A) in PDB entry 2A8L
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 GLY 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A SER 3.2 11.0 - - - -
297A LEU* 4.5 2.2 - - - -
302A LEU* 5.8 0.2 - - - -
323A MET* 4.1 3.5 - - - +
327A PHE* 3.6 21.2 - - - -
340A LEU* 1.3 74.8 - - - +
342A GLY* 1.3 58.4 + - - -
372A HIS* 3.2 2.8 - - - +
373A THR* 2.8 34.0 + - - -
374A THR* 3.6 12.2 + - - +
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Residues in contact with GLY 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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50A ALA* 4.0 3.9 - - - +
290A THR* 3.3 1.4 - - - -
291A SER 2.8 32.0 + - - +
297A LEU* 4.8 1.3 - - - +
323A MET* 4.9 0.7 - - - -
341A GLY* 1.3 73.5 - - - -
343A VAL* 1.3 70.8 + - - +
371A SER 3.2 10.8 - - - -
372A HIS* 3.7 8.7 - - - -
377A MET* 3.7 15.0 - - - -
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Residues in contact with VAL 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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288A VAL* 4.7 2.7 - - + -
289A SER 3.3 7.2 - - - +
290A THR* 3.6 22.2 - - + -
302A LEU* 3.6 22.4 - - + -
306A CYS* 4.3 11.0 - - - -
319A LEU* 4.2 17.7 - - + -
323A MET* 4.1 15.5 - - - -
342A GLY* 1.3 82.3 - - - +
344A ILE* 1.3 65.8 + - - +
345A VAL* 4.7 3.6 - - + -
370A TRP* 3.1 7.8 - - - +
371A SER* 2.8 50.3 + - - +
377A MET* 3.7 5.5 - - - +
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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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45A LEU* 3.5 44.0 - - + +
46A VAL* 4.0 3.6 - - - +
47A HIS* 3.7 39.0 - - + -
236A GLY 3.8 2.5 - - - +
237A ALA* 3.7 21.3 - - - +
238A VAL* 4.0 5.7 - - + +
287A ALA 4.0 0.2 - - - +
288A VAL* 3.5 1.9 - - - +
289A SER* 3.0 37.8 + - - +
343A VAL* 1.3 79.9 - - - +
345A VAL* 1.3 67.1 + - - +
369A LEU 3.4 3.8 - - - -
370A TRP* 4.2 2.5 - - + -
377A MET* 4.4 0.9 - - + -
379A VAL* 4.2 14.8 - - + -
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Residues in contact with VAL 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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45A LEU* 3.6 4.8 - - - +
238A VAL* 4.5 1.3 - - - -
287A ALA 3.4 4.9 - - - +
288A VAL* 3.8 23.8 - - + -
306A CYS* 4.4 7.6 - - + -
310A LEU* 3.1 39.9 - - + -
319A LEU* 4.6 13.9 - - + -
343A VAL* 4.7 5.6 - - + -
344A ILE* 1.3 80.0 - - - +
346A LEU* 1.3 72.3 + - - +
347A ARG* 4.6 0.9 - - + +
368A PHE* 3.2 7.5 - - - +
369A LEU* 2.7 50.9 + - + +
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Residues in contact with LEU 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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43A PHE* 4.0 11.9 - - + -
238A VAL* 3.8 18.6 - - + +
239A VAL* 3.6 39.5 - - - +
240A VAL* 3.8 16.4 - - + +
246A VAL* 3.7 28.5 - - + -
286A THR* 3.3 4.9 - - - -
287A ALA* 2.9 35.8 + - + +
345A VAL* 1.3 79.9 - - - +
347A ARG* 1.3 70.4 + - - +
348A SER* 4.3 4.7 - - - +
366A VAL* 4.0 13.0 - - + -
367A GLU 3.5 5.6 - - - -
368A PHE* 4.4 2.9 - - + +
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Residues in contact with ARG 347 (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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284A TYR* 3.3 49.3 + - + -
285A SER 3.3 3.6 - - - -
286A THR* 4.0 7.0 - - + -
310A LEU* 2.8 34.0 + - + -
312A ALA 2.8 27.7 + - - -
313A GLU 3.4 17.6 + - - -
315A ALA* 3.6 21.9 - - + +
345A VAL* 5.0 6.1 - - + -
346A LEU* 1.3 77.0 - - - +
348A SER* 1.3 61.0 + - - +
365A LEU 3.7 1.2 - - - +
366A VAL* 3.6 0.6 - - - -
367A GLU* 2.6 83.4 + - + +
369A LEU* 6.1 0.9 - - + -
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Residues in contact with SER 348 (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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240A VAL* 3.8 19.8 - - - +
244A GLY* 4.1 4.2 + - - -
246A VAL* 3.9 4.5 - - - +
278A THR* 4.2 0.9 + - - -
284A TYR* 3.9 6.3 - - - -
285A SER* 3.0 44.4 + - - -
346A LEU* 4.6 2.5 - - - -
347A ARG* 1.3 76.0 - - - +
349A CYS* 1.3 65.3 + - - +
364A LEU* 5.3 5.4 - - - -
365A LEU 3.2 13.2 - - - -
366A VAL* 3.9 18.6 - - - -
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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