Contacts of the helix formed by residues 525 - 534 (chain B) in PDB entry 1QAS
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 GLU 525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524B SER* 1.3 71.9 - - - +
526B SER* 1.3 61.4 + - - +
529B LEU* 3.0 43.1 + - + +
550B ILE* 4.1 2.7 - - - -
551B TYR 3.0 15.7 + - - +
552B PRO* 3.6 3.5 - - - +
553B ALA* 2.8 32.7 + - + +
555B TRP* 4.9 2.5 - - - -
556B ARG* 2.7 46.1 + - - -
562B TYR* 3.3 21.9 - - + +
567B MET* 3.5 22.3 - - + +
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Residues in contact with SER 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B SER* 2.8 21.2 + - - -
525B GLU* 1.3 84.0 - - - +
527B ARG* 1.3 59.5 + - - +
529B LEU* 3.4 11.1 + - - +
530B ARG* 3.1 25.6 + - - +
553B ALA* 5.2 6.3 - - - +
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Residues in contact with ARG 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B PHE* 3.4 46.5 + - - +
522B SER 3.3 23.6 + - - -
523B PHE* 3.7 23.0 - - + +
524B SER* 3.1 19.3 + - - +
526B SER* 1.3 78.4 + - - +
528B ALA* 1.3 61.6 + - - +
530B ARG* 3.0 34.3 + - - +
531B LEU* 2.8 38.5 + - + +
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Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B PHE* 4.0 8.4 - - + +
524B SER 2.9 16.9 + - - +
525B GLU 3.6 4.5 - - - +
527B ARG* 1.3 77.9 - - - +
529B LEU* 1.3 62.1 + - - +
531B LEU* 3.3 2.3 + - - +
532B LEU* 2.9 30.1 + - - +
539B PHE* 3.9 10.8 - - + -
550B ILE* 3.9 22.4 - - + -
567B MET* 3.7 24.0 - - + -
572B CYS* 5.5 0.2 - - - -
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B GLU* 3.0 33.8 + - + +
526B SER* 3.5 9.4 - - - +
528B ALA* 1.3 76.9 - - - +
530B ARG* 1.3 57.0 + - - +
532B LEU* 3.1 5.4 + - + +
533B GLN* 2.9 28.8 + - - +
566B GLU* 4.0 15.5 - - + -
567B MET* 3.9 18.8 - - + -
618B ARG* 3.4 28.7 + - - +
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Residues in contact with ARG 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B SER 3.1 12.5 + - - +
527B ARG* 3.0 40.5 + - - +
529B LEU* 1.3 77.4 - - - +
531B LEU* 1.3 68.9 + - - +
533B GLN* 3.1 7.4 + - - +
534B GLU* 2.8 66.3 + - + +
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Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B PHE* 4.0 18.4 - - + -
507B PHE* 4.0 20.0 - - + -
523B PHE* 3.1 43.3 - - + -
527B ARG* 2.8 25.6 + - + +
528B ALA 3.7 4.3 - - - +
530B ARG* 1.3 92.1 - - - +
532B LEU* 1.3 57.9 + - - +
534B GLU* 4.4 8.5 - - - +
535B SER* 2.8 37.4 + - - +
536B GLY 3.4 1.4 + - - -
539B PHE* 3.7 16.1 - - + -
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ALA* 2.9 24.4 + - + +
529B LEU* 3.1 9.8 + - - +
531B LEU* 1.3 76.3 - - - +
533B GLN* 1.3 61.1 + - - +
536B GLY* 3.3 25.5 + - - +
539B PHE* 3.3 28.7 - - + -
540B VAL* 5.5 0.2 - - + -
566B GLU* 3.4 42.6 - - + +
567B MET* 4.3 14.1 - - - +
570B GLY* 3.8 25.6 - - - -
572B CYS* 5.0 2.5 - - - -
616B ASN* 4.3 2.1 + - - +
618B ARG* 4.0 21.7 - - + +
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Residues in contact with GLN 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B LEU 2.9 12.1 + - - +
530B ARG* 3.7 7.4 - - - +
532B LEU* 1.3 78.9 - - - +
534B GLU* 1.3 62.3 + - + +
536B GLY 4.8 0.2 - - - -
618B ARG* 3.1 48.3 + - - +
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Residues in contact with GLU 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B ARG* 2.8 55.2 + - + +
531B LEU* 4.2 8.8 - - - +
533B GLN* 1.3 84.5 - - + +
535B SER* 1.3 65.4 + - - +
536B GLY 3.6 0.2 - - - -
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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