Contacts of the helix formed by residues 523 - 536 (chain A) in PDB entry 4H1S
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 523 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A GLY* 2.9 30.9 + - - +
419A GLY 3.6 8.7 + - - +
420A THR* 3.6 15.2 - - - +
522A ASP* 1.3 73.5 - - - +
524A ASP* 1.3 69.7 + - - +
525A ILE* 3.3 6.3 - - + +
526A ASN* 3.1 32.4 + - - +
527A VAL* 3.0 22.5 + - - +
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Residues in contact with ASP 524 (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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415A LEU* 4.5 16.4 - - + +
417A PHE* 4.6 5.5 + - - +
418A GLY* 3.9 10.3 + - - -
419A GLY* 2.7 48.7 + - - +
420A THR 4.7 0.2 - - - -
421A PHE* 3.3 48.7 - - + -
522A ASP 3.5 1.8 + - - -
523A GLN* 1.3 73.1 - - - +
525A ILE* 1.3 92.2 + - - +
528A VAL* 3.3 19.4 + - - +
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Residues in contact with ILE 525 (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 TRP* 4.0 31.6 - - + +
411A LEU* 4.0 20.2 - - + +
412A ALA* 3.6 37.0 - - + +
415A LEU* 4.0 22.4 - - + +
418A GLY* 5.9 2.7 - - - -
523A GLN* 5.1 6.5 - - + -
524A ASP* 1.3 95.6 + - - +
526A ASN* 1.3 78.6 + - - +
528A VAL* 3.4 0.9 + - - -
529A SER* 3.0 23.8 + - - -
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Residues in contact with ASN 526 (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 TRP* 3.4 21.7 - - - -
522A ASP* 6.1 0.9 - - + -
523A GLN* 3.1 32.5 + - + +
525A ILE* 1.3 81.4 - - - +
527A VAL* 1.3 65.7 + - + +
529A SER* 3.1 6.8 + - - -
530A THR* 2.9 33.9 + - - +
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Residues in contact with VAL 527 (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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367A ALA* 3.5 31.2 - - + +
368A MET* 4.1 2.0 - - - +
371A ASN* 3.6 24.7 - - + +
421A PHE* 3.7 29.4 - - + -
522A ASP* 3.6 26.5 - - + -
523A GLN 3.0 17.7 + - - +
524A ASP 3.5 7.6 - - - +
525A ILE 3.3 0.2 - - - -
526A ASN* 1.3 77.7 - - - +
528A VAL* 1.3 61.9 + - - +
530A THR* 3.5 4.9 + - - -
531A TYR* 3.1 22.2 + - - +
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Residues in contact with VAL 528 (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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360A MET* 6.5 0.2 - - - -
363A LEU* 4.9 10.1 - - + -
364A ILE* 4.1 21.5 - - + -
367A ALA* 4.2 19.1 - - + -
411A LEU* 3.9 22.4 - - + -
415A LEU* 3.7 20.6 - - + -
421A PHE* 4.0 12.6 - - + -
524A ASP 3.3 15.5 + - - +
525A ILE 3.4 3.3 + - - +
526A ASN 3.3 0.2 - - - -
527A VAL* 1.3 74.5 - - - +
529A SER* 1.3 61.0 + - - +
531A TYR* 3.4 1.8 + - + +
532A ILE* 3.0 38.5 + - + +
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Residues in contact with SER 529 (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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339A LEU* 3.7 15.8 - - - +
408A TRP* 3.3 27.4 - - - -
411A LEU* 3.6 19.9 - - - +
525A ILE 3.0 18.4 + - - -
526A ASN* 3.1 10.9 + - - -
528A VAL* 1.3 74.9 - - - +
530A THR* 1.3 60.7 + - - +
532A ILE* 3.4 4.5 + - - +
533A SER* 2.9 32.8 + - - -
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Residues in contact with THR 530 (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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371A ASN* 4.8 12.6 - - + +
526A ASN* 2.9 26.5 + - - +
527A VAL* 3.6 6.0 - - - -
529A SER* 1.3 78.0 + - - +
531A TYR* 1.3 52.8 + - - +
533A SER* 3.0 8.0 + - - -
534A LYS* 2.7 38.3 + - + +
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Residues in contact with TYR 531 (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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363A LEU* 3.7 28.9 - - + +
366A ASP* 4.1 17.3 + - + +
367A ALA* 3.7 28.3 - - + +
370A ASN* 3.7 37.0 - - + +
371A ASN* 6.0 1.6 - - + -
527A VAL 3.1 14.5 + - - +
528A VAL* 3.7 4.3 - - + +
529A SER 3.4 0.2 - - - -
530A THR* 1.3 78.7 - - - +
532A ILE* 1.3 63.5 + - + +
534A LYS* 3.4 6.3 + - - +
535A MET* 2.8 73.6 + - + +
538A ILE* 4.4 5.8 - - + -
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Residues in contact with ILE 532 (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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339A LEU* 3.8 11.6 - - + +
340A GLY* 3.7 27.1 - - - +
341A LYS 4.5 1.6 - - - +
346A LEU* 5.8 0.9 - - + -
363A LEU* 4.8 5.2 - - + -
398A ILE* 6.2 0.7 - - + -
406A ILE* 4.3 25.6 - - + -
411A LEU* 4.5 11.7 - - + -
528A VAL* 3.0 38.7 + - + +
529A SER* 3.8 4.7 - - - +
530A THR 3.2 0.4 - - - -
531A TYR* 1.3 82.4 - - + +
533A SER* 1.3 57.4 + - - +
535A MET* 3.8 0.7 - - - +
536A LYS* 2.9 28.9 + - - -
538A ILE* 4.0 35.4 - - + +
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Residues in contact with SER 533 (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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339A LEU* 3.1 30.9 + - - +
529A SER 2.9 15.6 + - - -
530A THR* 3.4 10.3 - - - -
532A ILE* 1.3 75.0 - - - +
534A LYS* 1.3 65.3 + - - +
536A LYS* 3.1 31.1 + - - +
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Residues in contact with LYS 534 (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 ARG* 4.0 32.1 - - - +
530A THR* 2.7 23.9 + - + +
531A TYR* 3.7 7.2 - - - +
533A SER* 1.3 74.0 - - - +
535A MET* 1.3 64.1 + - + +
536A LYS* 3.4 11.4 + - - +
374B ARG* 3.7 8.0 + - - -
534B LYS* 5.1 8.9 - - - +
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Residues in contact with MET 535 (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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370A ASN* 3.9 2.9 - - - +
374A ARG* 3.4 22.9 - - - +
531A TYR* 2.8 67.0 + - + +
534A LYS* 1.3 73.2 - - + +
536A LYS* 1.3 59.6 + - - +
537A VAL 2.7 22.1 + - - +
538A ILE* 3.9 18.8 - - + -
370B ASN* 5.4 4.5 - - - +
374B ARG* 2.9 26.8 + - - +
535B MET* 3.4 44.2 - - + +
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Residues in contact with LYS 536 (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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340A GLY* 3.8 5.3 - - - -
341A LYS* 3.0 27.7 + - - +
532A ILE 2.9 16.1 + - - -
533A SER* 3.1 28.8 + - - +
534A LYS* 3.3 12.7 + - - +
535A MET* 1.3 75.7 - - - +
537A VAL* 1.3 68.2 + - + +
538A ILE* 5.3 0.7 - - - -
374B ARG* 3.5 17.7 - - + +
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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