Contacts of the strand formed by residues 375 - 383 (chain A) in PDB entry 4RQE
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 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A HIS* 4.3 7.1 + - + +
142A SER* 3.0 32.3 + - - +
143A VAL* 3.8 17.0 - - + -
338A TRP* 3.7 30.6 - - + -
341A PHE* 4.2 15.9 - - + -
342A GLU* 4.3 15.6 + - - -
363A ASN* 4.2 10.9 - - - +
373A ALA* 3.6 2.4 - - - +
374A SER* 1.3 82.6 - - - +
376A LYS* 1.3 63.4 + - - +
377A LEU* 4.0 32.7 + - + +
395A CYS 4.0 0.5 - - - +
396A SER* 3.6 3.1 - - - -
397A ASN* 3.3 24.3 + - - +
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Residues in contact with LYS 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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143A VAL* 5.0 1.4 - - - +
363A ASN* 4.0 3.9 + - - +
364A ILE* 3.3 44.6 + - + +
369A LEU* 5.2 10.5 - - + -
373A ALA* 4.7 9.0 - - + -
375A LYS* 1.3 76.2 - - - +
377A LEU* 1.3 64.0 + - - +
378A ASP 3.6 1.0 + - - -
394A SER* 5.1 5.8 - - - +
395A CYS 3.4 10.8 - - - +
396A SER* 4.2 9.2 - - - +
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Residues in contact with LEU 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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156A THR* 5.1 5.4 - - + +
341A PHE* 3.6 35.3 - - + -
342A GLU* 4.9 7.4 - - - +
345A ILE* 4.3 18.4 - - + +
361A ILE* 4.6 19.3 - - + -
362A VAL 3.6 5.2 - - - +
363A ASN* 3.4 45.3 - - + +
375A LYS* 4.0 17.1 + - - +
376A LYS* 1.3 70.4 - - - +
378A ASP* 1.3 60.8 + - - +
379A LEU 4.2 0.3 + - - -
393A VAL* 5.3 0.3 - - - +
395A CYS* 3.1 31.4 + - + +
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Residues in contact with ASP 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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361A ILE* 5.2 1.8 - - - -
362A VAL* 2.9 41.9 + - - +
364A ILE* 3.2 30.8 - - + +
376A LYS 3.6 2.0 + - - -
377A LEU* 1.3 73.9 - - - +
379A LEU* 1.3 59.0 + - - +
380A GLU* 4.6 5.4 - - - +
391A GLU* 2.8 33.4 - - - +
393A VAL 3.1 17.7 - - - +
394A SER* 3.4 19.5 - - - +
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Residues in contact with LEU 379 (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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345A ILE* 5.4 6.7 - - + -
348A ALA* 5.1 5.4 - - + +
349A GLU* 5.0 6.1 - - + -
352A TYR* 4.9 17.7 - - + -
359A TYR* 3.5 53.4 - - + -
360A HIS 3.9 3.4 - - - +
361A ILE* 3.9 14.6 - - + +
362A VAL 4.7 0.7 - - - +
377A LEU 4.2 0.6 + - - -
378A ASP* 1.3 72.3 - - - +
380A GLU* 1.3 63.3 + - - +
381A ALA* 4.2 8.1 - - + +
391A GLU* 3.3 4.5 - - - -
392A LEU* 2.7 35.9 + - + -
393A VAL* 3.1 39.5 + - + +
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Residues in contact with GLU 380 (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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153A ASN* 5.7 1.6 + - - -
359A TYR* 3.4 1.6 - - - +
360A HIS* 2.9 69.6 + - + +
362A VAL* 3.4 18.8 - - + +
378A ASP* 4.0 6.8 + - - +
379A LEU* 1.3 77.9 - - - +
381A ALA* 1.3 61.2 + - - +
389A PHE* 4.0 19.3 - - + +
390A ARG 3.7 4.0 - - - +
391A GLU* 3.7 26.0 + - + +
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Residues in contact with ALA 381 (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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352A TYR* 6.3 0.7 - - + -
357A ILE* 4.4 12.1 - - + -
358A PRO 3.9 9.6 - - - +
359A TYR* 4.2 1.6 - - + +
379A LEU* 4.2 6.9 - - + +
380A GLU* 1.3 73.9 - - - +
382A TRP* 1.3 64.6 + - - +
383A PHE* 3.6 9.6 - - + -
389A PHE* 3.3 5.6 - - - -
390A ARG 2.9 30.9 + - - +
392A LEU* 3.6 32.8 - - + -
439A ALA* 5.2 1.3 - - + -
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Residues in contact with TRP 382 (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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161A ASP 4.9 2.0 - - - -
162A CYS* 4.3 21.1 - - + -
163A THR* 5.6 1.1 - - - -
164A VAL* 2.8 34.8 + - + +
165A ARG* 3.9 16.4 - - + -
357A ILE* 4.9 1.7 - - - +
358A PRO* 3.1 35.7 + - + +
381A ALA* 1.3 73.7 - - - +
383A PHE* 1.3 74.4 + - - +
384A PRO* 3.3 25.4 - - + +
387A GLY* 3.5 19.7 - - - -
388A ALA* 3.3 35.0 - - - -
389A PHE* 3.5 41.7 - + + -
439A ALA* 5.5 0.5 - - - +
443A ASN* 3.4 15.2 + - - +
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Residues in contact with PHE 383 (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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170A HIS* 3.7 21.5 - + - -
316A PHE* 4.2 18.8 - + - -
381A ALA* 3.6 17.7 - - + -
382A TRP* 1.3 78.4 - - - +
384A PRO* 1.3 58.1 - - - +
386A SER* 3.7 19.7 - - - -
387A GLY* 2.5 36.0 + - - -
388A ALA* 2.6 18.3 + - + +
390A ARG* 3.7 29.2 - - + -
392A LEU* 5.3 2.0 - - + -
435A ARG 4.3 3.1 - - - -
438A CYS* 3.8 19.5 - - + -
439A ALA* 4.0 27.4 - - + -
442A GLU* 3.2 24.0 - - + +
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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