Contacts of the strand formed by residues 423 - 431 (chain A) in PDB entry 4NEH
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 GLN 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A GLN* 3.4 3.0 - - - -
420A VAL* 2.8 42.4 + - - +
421A SER* 3.4 2.4 - - - -
422A ARG* 1.3 81.6 - - - +
424A TRP* 1.3 70.7 + - - +
425A ARG* 3.6 31.4 + - + +
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Residues in contact with TRP 424 (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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344A ASP* 5.9 2.2 - - - -
347A VAL* 6.4 0.9 - - + -
362A LEU* 3.9 16.2 - - + +
370A THR* 3.5 25.0 + - - -
371A PHE 5.0 4.7 - - - +
372A ILE* 3.4 49.8 - - + +
373A ASN 5.1 5.9 - - - +
399A GLN* 4.2 23.1 - - + -
400A SER 5.5 0.2 - - - -
401A LEU* 4.4 9.9 - - + -
417A PHE* 3.4 33.7 - - + -
418A THR* 3.5 31.4 - - - -
419A GLN* 3.0 37.6 - - + +
422A ARG 5.0 2.9 - - - -
423A GLN* 1.3 83.5 + - - +
425A ARG* 1.3 65.5 + - - +
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Residues in contact with ARG 425 (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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373A ASN 6.0 0.4 - - - -
375A SER* 5.0 16.2 + - - -
377A GLU* 5.2 4.4 + - - -
417A PHE* 3.8 6.2 - - - -
418A THR* 3.1 33.9 + - - +
420A VAL* 5.1 17.0 - - + +
423A GLN* 3.6 29.9 + - + +
424A TRP* 1.3 80.3 + - - +
426A MET* 1.3 68.7 + - - +
427A LYS 3.5 0.2 + - - -
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Residues in contact with MET 426 (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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374A MET* 4.5 11.2 - - + -
415A VAL* 3.6 22.2 - - + -
416A ILE 3.7 5.8 - - - +
417A PHE* 3.8 17.2 - - + -
425A ARG* 1.3 76.4 - - - +
427A LYS* 1.3 70.5 + - - +
428A ALA* 4.0 5.6 - - - +
429A GLU* 3.4 32.8 - - - +
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Residues in contact with LYS 427 (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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395A TRP* 3.8 31.9 - - + -
416A ILE 2.9 15.6 + - - +
418A THR* 4.2 28.0 - - + +
425A ARG 3.5 0.6 + - - -
426A MET* 1.3 85.0 - - - +
428A ALA* 1.3 59.1 + - + +
482A TRP* 4.4 26.4 - - - +
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Residues in contact with ALA 428 (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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395A TRP* 4.5 9.6 - - + -
415A VAL* 3.5 2.8 - - - +
416A ILE* 2.9 38.5 + - + +
426A MET* 4.5 2.0 - - - -
427A LYS* 1.3 81.1 - - + +
429A GLU* 1.3 68.8 + - - +
479A PRO* 5.2 2.0 - - + -
485A TRP* 3.8 34.1 - - + +
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Residues in contact with GLU 429 (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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374A MET* 3.2 31.0 - - - +
413A LYS* 3.2 28.2 + - + +
414A ALA 3.4 7.0 - - - +
415A VAL* 3.8 13.0 - - + -
426A MET* 3.4 20.0 - - - +
428A ALA* 1.3 80.5 - - - +
430A VAL* 1.3 65.4 + - - +
431A THR* 5.4 3.0 + - - +
484A ARG* 5.1 7.1 + - - +
485A TRP* 3.5 21.0 + - - +
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Residues in contact with VAL 430 (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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413A LYS* 3.1 3.7 - - - +
414A ALA* 2.9 37.3 + - + +
429A GLU* 1.3 76.6 - - - +
431A THR* 1.3 71.9 + - - +
439A PHE* 3.6 3.4 - - + -
459A ILE* 3.6 24.0 - - + -
476A CYS* 4.5 0.9 - - - -
485A TRP* 3.5 33.0 - - + +
486A TRP* 4.2 9.0 - - - -
487A CYS* 3.6 35.2 - - + +
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Residues in contact with THR 431 (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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408A TYR* 4.4 13.2 - - + -
411A THR* 4.1 8.5 - - - +
412A GLY 3.6 10.3 - - - +
413A LYS* 3.8 14.8 - - + +
429A GLU* 5.4 2.9 + - - +
430A VAL* 1.3 84.9 + - - +
432A GLY* 1.3 76.1 + - - +
433A THR* 4.7 5.4 - - - +
439A PHE* 3.9 9.6 - - - -
484A ARG* 5.9 0.7 + - - -
487A CYS* 5.6 0.9 - - - -
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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