Contacts of the strand formed by residues 369 - 378 (chain A) in PDB entry 5DQE
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 ARG 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A GLN* 4.7 5.9 - - - +
334A GLU* 2.7 34.0 + - + -
335A SER 3.8 10.5 - - - +
336A LEU* 4.4 11.4 - - + +
365A LEU* 3.7 6.2 - - - +
366A GLU* 2.9 65.7 + - - +
367A ASP* 4.1 20.7 + - - +
368A GLY* 1.3 78.3 - - - +
370A PHE* 1.3 66.6 + - - +
371A VAL* 3.3 21.5 - - + +
373A ARG* 4.6 3.2 - - - +
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Residues in contact with PHE 370 (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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334A GLU* 3.1 7.4 - - - +
335A SER 2.7 38.1 + - - +
336A LEU* 3.5 22.4 - - - -
337A GLU 3.5 17.0 - - - +
338A HIS* 3.6 42.6 - + + -
363A ALA* 3.9 20.2 - - + -
364A GLN 3.3 1.1 - - - -
365A LEU* 3.9 38.6 - - + -
369A ARG* 1.3 75.3 - - - +
371A VAL* 1.3 61.6 + - - +
372A TYR* 3.8 10.8 - - - +
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Residues in contact with VAL 371 (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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332A GLN* 4.0 20.2 - - + +
333A TYR 3.4 7.9 - - - +
334A GLU* 4.4 2.0 - - + -
362A ARG 4.1 0.7 - - - +
363A ALA 3.7 0.5 - - - -
364A GLN* 2.8 51.7 + - + +
366A GLU* 4.1 10.5 - - + +
369A ARG* 3.3 37.0 - - + +
370A PHE* 1.3 75.5 - - - +
372A TYR* 1.3 66.0 + - - +
373A ARG* 3.6 32.1 + - + +
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Residues in contact with TYR 372 (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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228A LEU* 4.2 6.3 - - + -
332A GLN* 3.2 5.5 - - - -
333A TYR* 2.9 46.0 + - + +
334A GLU* 4.2 0.2 - - - -
335A SER* 3.1 20.7 + - - -
337A GLU 3.0 23.7 + - - -
339A MET* 3.0 41.1 + - + +
341A LEU* 3.6 38.8 - - + -
361A GLU* 3.9 17.7 - - + -
362A ARG 4.0 1.8 - - - -
363A ALA* 3.4 26.4 - - + +
370A PHE* 3.8 14.5 - - - +
371A VAL* 1.3 73.7 - - - +
373A ARG* 1.3 61.0 + - - +
374A LEU* 3.5 10.9 - - + +
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Residues in contact with ARG 373 (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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331A SER 3.8 3.1 - - - -
332A GLN* 3.0 47.6 + - + +
361A GLU* 3.4 23.3 + - - +
364A GLN* 5.0 5.7 - - - +
366A GLU* 2.5 43.2 + - - -
369A ARG* 4.6 1.0 - - - +
371A VAL* 3.6 18.0 + - + +
372A TYR* 1.3 71.3 - - - +
374A LEU* 1.3 61.5 + - - +
375A LEU* 3.6 31.7 + - + +
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Residues in contact with LEU 374 (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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329A VAL 3.7 3.1 - - - +
330A SER* 3.3 4.9 - - - -
331A SER* 2.9 48.6 + - - +
333A TYR* 4.0 16.2 - - + -
341A LEU* 5.7 0.4 - - + -
343A CYS* 3.6 31.0 - - + -
359A GLU* 4.6 25.4 - - + +
360A THR 5.5 0.2 - - - -
361A GLU* 4.1 26.5 - - + +
372A TYR* 3.5 22.0 - - + +
373A ARG* 1.3 72.5 - - - +
375A LEU* 1.3 60.6 + - - +
377A SER* 4.7 6.0 + - - -
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Residues in contact with LEU 375 (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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330A SER* 3.5 15.7 - - - +
331A SER 4.1 9.4 - - - +
332A GLN* 4.8 7.0 - - + +
373A ARG* 3.6 41.5 + - + -
374A LEU* 1.3 76.0 - - - +
376A ARG* 1.3 77.0 + - + +
377A SER* 3.2 5.0 + - - -
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Residues in contact with ARG 376 (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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236A PHE* 4.1 10.7 - - + -
238A GLU* 2.3 41.0 + - - -
248A ARG* 3.6 25.1 - - - +
326A PHE* 3.4 44.8 - - + +
329A VAL 3.3 4.5 + - - +
330A SER* 2.7 15.9 + - - +
375A LEU* 1.3 79.6 - - + +
377A SER* 1.3 64.8 + - - +
378A PRO* 3.3 9.4 - - - +
418B GLN* 5.2 1.7 + - - -
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Residues in contact with SER 377 (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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328A GLY* 3.3 1.2 - - - -
329A VAL* 2.8 41.7 + - - +
357A LYS* 2.8 28.5 + - - -
359A GLU* 3.0 25.8 + - - -
374A LEU* 4.9 7.6 - - - -
375A LEU 3.2 4.3 + - - -
376A ARG* 1.3 71.3 - - - +
378A PRO* 1.3 71.8 + - - +
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Residues in contact with PRO 378 (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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326A PHE* 4.0 16.8 - - + -
327A TYR 3.5 8.1 - - - +
357A LYS* 3.0 19.6 + - - -
376A ARG 3.3 9.4 - - - +
377A SER* 1.3 82.6 - - - +
379A MET* 1.3 70.3 + - - +
380A CYS* 3.4 1.6 + - - -
415B ARG* 5.6 3.6 - - + +
418B GLN* 3.1 38.4 - - - +
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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