Contacts of the strand formed by residues 521 - 529 (chain B) in PDB entry 4QDQ
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 VAL 521 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503B ILE* 3.9 22.2 - - + -
520B PHE* 1.3 74.6 - - - +
522B ARG* 1.3 56.4 + - - +
523B LYS 3.3 26.0 - - - +
524B PHE* 4.1 4.3 - - + -
551B GLY* 3.5 1.7 - - - -
552B ASN* 2.8 38.1 + - - +
575B PRO* 3.9 17.7 - - + -
577B ARG 3.5 6.1 - - - +
578B TRP* 4.1 2.7 - - + +
583B ILE* 3.9 29.6 - - + -
584B GLY 3.7 11.2 + - - +
585B MET* 4.0 15.9 - - + +
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Residues in contact with ARG 522 (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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520B PHE* 3.7 35.0 - - + -
521B VAL* 1.3 73.2 - - - +
523B LYS* 1.3 62.1 + - + +
550B GLU* 3.4 9.7 + - - +
551B GLY* 2.7 26.0 + - - -
552B ASN 4.0 9.5 + - - +
553B MET* 5.1 9.2 - - - +
577B ARG* 2.6 24.7 + - + +
578B TRP* 3.7 23.8 - - - +
579B SER* 4.0 5.2 - - - +
580B PRO* 5.6 1.8 - - - -
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Residues in contact with LYS 523 (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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521B VAL* 3.3 3.7 - - - +
522B ARG* 1.3 80.2 - - + +
524B PHE* 1.3 61.6 + - - +
548B LEU* 4.5 22.4 + - + +
549B PHE 3.3 17.7 - - - +
550B GLU* 2.6 38.7 + - - +
551B GLY 4.2 0.7 - - - +
576B GLU* 2.7 34.9 + - + -
577B ARG* 2.9 48.3 + - + +
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Residues in contact with PHE 524 (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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501B VAL* 4.0 17.9 - - + -
503B ILE* 3.8 26.2 - - + -
521B VAL* 4.1 4.3 - - + -
523B LYS* 1.3 79.0 - - - +
525B LYS* 1.3 63.2 + - - +
526B VAL* 3.5 28.5 - - + -
547B LYS 3.6 1.2 - - - +
548B LEU* 3.7 1.7 - - - -
549B PHE* 2.8 54.9 + + + +
550B GLU 3.3 23.8 - - - -
551B GLY* 4.0 8.5 - - - -
561B ARG* 4.0 14.6 - - + -
573B VAL* 3.6 29.6 - - + -
574B TYR 3.2 15.3 - - - +
575B PRO* 4.0 3.1 - - + -
576B GLU* 4.0 2.9 - - - +
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Residues in contact with LYS 525 (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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484B GLY* 5.6 4.4 - - - -
524B PHE* 1.3 78.6 - - - +
526B VAL* 1.3 64.7 + - - +
527B SER 4.3 0.2 - - - -
537B TYR* 3.9 23.1 - - + +
545B GLN* 5.1 5.5 + - - -
546B PRO* 3.9 29.3 + - + +
547B LYS 3.6 17.7 - - - +
548B LEU* 3.7 18.6 - - + -
573B VAL* 3.6 4.2 - - - -
574B TYR* 2.8 43.4 + - + +
576B GLU* 3.6 33.8 + - + +
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Residues in contact with VAL 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B VAL* 4.8 5.6 - - + -
524B PHE* 3.5 28.0 - - + -
525B LYS* 1.3 80.5 - - - +
527B SER* 1.3 69.3 + - - +
528B TYR* 5.5 1.1 - - + -
537B TYR* 3.3 8.9 - - - -
538B ILE* 3.0 54.2 + - + +
547B LYS 4.6 0.6 + - - -
549B PHE* 3.7 20.1 - - + -
563B PHE* 4.7 11.7 - - + -
571B VAL* 4.1 14.8 - - + -
572B ARG 3.4 11.2 - - - +
573B VAL* 4.7 4.7 - - + -
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Residues in contact with SER 527 (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 LYS 4.3 0.2 - - - -
526B VAL* 1.3 75.3 - - - +
528B TYR* 1.3 62.9 + - - +
535B TRP* 3.5 15.2 - - - -
536B GLU 3.2 13.7 - - - -
537B TYR* 3.9 25.3 - - - -
571B VAL* 3.5 4.7 - - - +
572B ARG* 2.8 38.7 + - - +
574B TYR* 3.2 22.4 + - - -
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Residues in contact with TYR 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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526B VAL* 5.6 1.1 - - + -
527B SER* 1.3 78.2 - - - +
529B SER* 1.3 63.1 + - - +
530B LEU 5.4 0.4 - - - -
534B ASP 4.0 0.2 - - - +
535B TRP* 3.4 8.9 - - - -
536B GLU* 2.8 70.5 + - + +
537B TYR 4.1 2.7 + - - -
538B ILE* 3.9 34.0 - - + -
566B ILE* 3.5 49.1 - - + +
567B PRO* 3.8 19.1 - - + -
568B ALA* 3.9 9.0 - - + -
570B TYR 3.3 12.3 - - - +
571B VAL* 4.6 6.5 - - + -
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Residues in contact with SER 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B TYR* 1.3 77.2 - - - +
530B LEU* 1.3 61.1 + - - +
531B ASN 3.5 0.7 + - - -
532B GLY* 2.8 32.5 + - - -
533B LYS 3.6 0.2 + - - -
534B ASP 2.6 24.5 + - - -
535B TRP* 3.5 28.0 - - - -
567B PRO 4.9 0.2 - - - -
568B ALA* 4.1 3.8 - - - -
569B GLN 2.9 21.5 + - - -
570B TYR* 3.0 19.2 + - - -
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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