Contacts of the strand formed by residues 532 - 537 (chain A) in PDB entry 1Q2L
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 LEU 532 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A VAL* 3.8 21.3 - - + +
529A GLU* 2.8 36.2 + - + +
530A SER 3.7 0.6 - - - -
531A ASN* 1.3 87.1 - - - +
533A ARG* 1.3 72.5 + - - +
534A VAL* 4.3 7.4 - - + -
699A ARG* 4.3 2.0 - - - +
700A PRO* 3.6 19.1 - - + +
702A PHE* 3.9 27.1 - - + -
717A ALA* 4.5 3.6 - - + +
718A ARG* 3.6 38.1 - - + +
721A GLN* 3.4 23.8 - - - +
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Residues in contact with ARG 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LEU* 4.0 17.1 - - + +
527A VAL 3.3 2.9 - - - -
528A ASP* 2.8 33.6 + - - +
529A GLU 2.9 20.9 + - - +
530A SER* 4.8 2.8 - - - +
532A LEU* 1.3 79.0 - - - +
534A VAL* 1.3 66.2 + - - +
535A VAL* 4.2 2.9 - - + -
699A ARG* 3.3 40.3 - - - +
700A PRO 3.2 6.6 + - - +
701A GLU* 3.4 29.7 + - + +
702A PHE* 2.8 27.4 + - - -
880A PHE* 6.0 0.9 - - + -
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LEU* 3.4 3.6 - - - -
526A ILE* 2.8 33.2 + - + -
527A VAL* 2.9 34.3 + - + -
532A LEU* 4.3 6.7 - - + -
533A ARG* 1.3 79.6 - - - +
535A VAL* 1.3 67.6 + - - +
536A TYR* 4.9 4.0 - - + -
702A PHE* 3.5 14.8 - - + -
704A VAL* 5.1 2.2 - - + -
713A ALA* 4.6 25.6 - - + +
714A THR* 4.8 7.0 - - + -
717A ALA* 3.4 29.4 - - + -
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Residues in contact with VAL 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PRO* 3.6 25.1 - - + -
524A GLU 3.3 9.2 - - - +
525A LEU* 4.2 9.4 - - + -
533A ARG* 5.5 1.8 - - + -
534A VAL* 1.3 78.6 - - - +
536A TYR* 1.3 65.6 + - - +
702A PHE 2.8 11.4 + - - +
703A MET* 3.3 10.4 - - + -
704A VAL 2.8 26.0 + - - -
880A PHE* 3.6 28.9 - - + -
885A MET* 3.7 22.7 - - + -
887A PHE* 3.7 17.7 - - + -
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Residues in contact with TYR 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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516A SER* 2.9 21.4 + - - -
520A TYR* 3.6 21.2 - + - -
523A PRO* 4.1 2.0 - - - -
524A GLU 2.7 32.5 + - - +
526A ILE* 3.6 18.4 - - + -
534A VAL* 4.9 6.1 - - + -
535A VAL* 1.3 77.2 - - - +
537A ALA* 1.3 77.9 + - - +
538A PRO* 3.8 14.3 - - + +
704A VAL* 3.4 17.3 - - + -
705A ILE* 4.7 0.7 - - - -
706A GLY 4.5 2.9 - - - -
708A MET 2.6 31.1 + - - -
709A THR* 3.7 11.3 - - - -
710A GLU* 3.4 40.5 + - + -
713A ALA* 4.0 18.8 - - + -
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Residues in contact with ALA 537 (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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520A TYR* 4.3 6.3 - - + -
522A HIS* 4.4 4.0 - - - -
523A PRO* 3.5 31.0 - - + -
536A TYR* 1.3 89.3 - - - +
538A PRO* 1.3 79.5 - - + +
540A ARG* 6.1 2.9 - - + -
704A VAL 3.1 4.6 + - - +
705A ILE* 3.1 15.5 - - + +
706A GLY 3.0 16.1 + - - -
876A LEU* 5.9 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