Contacts of the strand formed by residues 424 - 432 (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 HIS 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A SER* 3.2 35.0 + - - +
332A PRO* 3.9 28.8 + - + +
337A SER* 3.9 34.5 - - - -
338A TRP* 5.6 3.8 - + - -
397A ASN* 4.5 4.9 - - - +
399A THR* 3.4 30.6 - - + +
400A ASP* 3.5 27.0 + - + -
422A PHE 3.8 1.7 + - - -
423A VAL* 1.3 84.2 + - - +
425A MET* 1.3 63.4 + - - +
426A LEU* 3.9 2.6 - - + +
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Residues in contact with MET 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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277A ALA* 4.5 6.1 - - + +
327A PHE* 4.7 12.3 - - + -
328A VAL 4.0 4.5 - - - +
329A TYR* 3.4 36.8 - - + -
398A CYS* 2.8 30.7 + - + +
399A THR 2.9 17.8 + - - +
402A GLN* 3.5 39.9 - - + +
403A ALA* 3.6 16.8 - - + +
406A LEU* 4.2 14.6 - - + -
408A ILE* 4.2 10.1 - - - -
423A VAL* 4.0 11.7 - - + -
424A HIS* 1.3 77.8 - - - +
426A LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 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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327A PHE* 3.3 23.0 - - - -
328A VAL* 3.4 33.9 + - + +
330A SER* 3.9 21.1 - - - +
337A SER* 4.0 6.7 - - - +
340A MET* 5.2 2.9 - - + -
341A PHE* 3.6 38.6 - - + +
344A MET* 3.9 15.3 - - + -
396A SER 3.3 7.4 - - - +
397A ASN* 3.5 35.9 - - + +
398A CYS* 4.3 0.9 - - - +
424A HIS* 3.9 5.6 - - + +
425A MET* 1.3 79.9 - - - +
427A ASN* 1.3 64.9 + - - +
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Residues in contact with ASN 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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273A GLU* 2.6 35.8 + - + -
325A GLU* 3.2 12.1 - - - +
326A GLN 3.3 7.9 - - - -
327A PHE* 3.7 15.9 - - + -
344A MET* 4.2 2.9 - - - +
394A SER 3.8 0.9 - - - +
395A CYS* 3.5 0.3 - - - -
396A SER* 2.6 58.3 + - - +
398A CYS* 3.5 12.7 - - - -
426A LEU* 1.3 76.2 - - - +
428A ALA* 1.3 57.7 - - - +
601A SER* 2.9 21.2 + - - +
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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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325A GLU* 3.2 7.9 + - - -
326A GLN* 2.7 56.6 + - + +
344A MET* 3.9 8.5 - - + -
345A ILE* 6.3 0.2 - - - -
393A VAL* 5.2 2.9 - - + -
394A SER 3.7 6.5 - - - -
395A CYS* 3.6 30.3 - - + +
427A ASN* 1.3 75.3 - - - +
429A THR* 1.3 61.6 + - - +
601A SER* 4.0 0.2 - - - -
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Residues in contact with THR 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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323A LYS* 3.2 30.2 - - - +
324A ILE 3.8 0.4 - - - -
325A GLU* 3.3 11.7 - - - -
326A GLN* 4.5 2.3 - - - +
348A ALA* 5.3 1.2 - - - +
352A TYR* 5.1 0.2 - - - -
392A LEU 4.0 2.0 - - - +
393A VAL* 3.3 22.5 - - - +
394A SER 3.4 11.8 + - - +
428A ALA* 1.3 70.4 - - - +
430A MET* 1.3 63.7 + - - +
431A CYS 3.4 10.0 + - - -
432A ALA 3.8 0.9 + - - -
601A SER* 3.1 28.9 + - - +
602A ANP 3.4 28.3 - - - +
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Residues in contact with MET 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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211A ALA* 4.7 14.1 - - + -
214A THR* 4.5 9.6 - - + -
215A LEU* 3.7 40.4 - - + -
324A ILE* 2.8 21.1 + - + +
326A GLN* 3.5 31.4 - - + +
347A THR* 4.4 9.4 - - + +
348A ALA* 4.6 7.4 - - - -
351A PHE* 3.5 43.5 - - + -
352A TYR* 3.0 27.4 + - - -
428A ALA 3.2 4.4 + - - -
429A THR* 1.3 72.5 - - - +
431A CYS* 1.3 62.5 + - - +
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Residues in contact with CYS 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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207A LEU* 3.5 22.9 - - - -
211A ALA* 4.7 7.4 - - + -
323A LYS* 3.2 4.3 - - - +
324A ILE* 3.0 37.2 + - + +
351A PHE* 4.5 10.3 - - + -
352A TYR* 3.3 9.4 - - - +
392A LEU 5.4 0.4 - - - -
429A THR* 3.3 6.4 - - - -
430A MET* 1.3 86.3 - - + +
432A ALA* 1.3 63.1 + - - +
433A THR* 3.6 10.6 + - - -
436A THR* 3.4 27.1 - - - -
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Residues in contact with ALA 432 (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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322A GLU 4.2 1.1 - - - -
323A LYS* 3.8 9.9 - - + -
352A TYR* 4.3 3.0 + - - -
392A LEU* 4.4 5.5 + - + -
429A THR* 3.8 2.6 + - - -
431A CYS* 1.3 69.1 - - - +
433A THR* 1.3 53.1 + - - +
434A THR 3.0 4.8 + - - -
435A ARG* 4.2 11.7 - - + -
436A THR* 2.4 36.8 + - - +
602A ANP 3.1 51.1 + - + +
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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