Contacts of the strand formed by residues 531 - 538 (chain A) in PDB entry 3L5J
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 ASN 531 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A ILE* 3.6 4.2 - - - +
530A ARG* 1.3 92.7 + - - +
532A TYR* 1.3 68.8 + - - +
533A THR* 4.1 2.4 + - - -
547A ASN* 4.7 15.8 + - + +
548A VAL 3.4 16.4 - - - +
549A ASP* 5.1 1.1 - - - -
550A SER* 4.1 6.1 - - - +
572A ALA* 4.0 1.2 - - - -
573A TYR* 3.1 49.2 + - - +
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Residues in contact with TYR 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A PRO* 3.8 20.6 - - + -
517A TRP* 3.7 18.9 + + - -
519A GLN* 4.1 26.0 - - - +
520A LEU* 3.9 24.3 + - + +
529A ILE* 4.5 15.0 - - + +
531A ASN* 1.3 79.9 - - - +
533A THR* 1.3 69.7 + - - +
547A ASN* 3.8 2.1 - - - -
548A VAL* 3.0 33.5 + - + +
549A ASP 3.4 14.6 - - - -
550A SER* 3.4 32.4 + - - -
552A HIS 3.6 15.7 + - - -
570A MET* 3.6 18.8 - - + -
571A ALA 3.1 9.9 - - - +
572A ALA* 4.4 4.3 - - + -
573A TYR* 4.3 0.2 - - - -
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Residues in contact with THR 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A ASN* 4.1 1.6 + - - -
532A TYR* 1.3 80.3 + - - +
534A ILE* 1.3 64.0 + - - +
535A PHE* 3.4 35.8 - - + -
545A ALA* 4.3 11.9 - - + -
546A VAL 3.2 10.8 - - - +
547A ASN* 3.3 15.9 + - - +
570A MET* 3.3 4.7 - - - -
571A ALA 2.9 32.3 + - - -
573A TYR* 3.1 28.9 - - - +
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Residues in contact with ILE 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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515A LEU* 4.4 10.8 - - + -
517A TRP* 4.3 10.3 - - + -
533A THR* 1.3 73.8 - - - +
535A PHE* 1.3 64.4 + - - +
536A TYR* 4.4 9.9 - - + -
544A THR 3.4 2.3 - - - +
545A ALA* 3.3 4.6 - - - -
546A VAL* 2.9 37.5 + - + +
548A VAL* 3.6 29.4 - - + -
555A TYR* 3.6 35.9 - - + -
557A LEU* 4.9 3.1 - - + -
568A VAL* 3.7 26.2 - - + -
569A ARG 3.8 2.2 - - - -
570A MET* 4.0 20.0 - - + -
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Residues in contact with PHE 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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533A THR* 3.4 35.7 - - + -
534A ILE* 1.3 73.6 - - - +
536A TYR* 1.3 65.3 + - - +
543A GLU* 3.5 34.8 - - + +
544A THR 3.3 4.0 - - - -
545A ALA* 3.9 19.7 - - + -
567A MET 3.8 0.6 - - - +
568A VAL* 3.3 5.2 - - - +
569A ARG* 2.9 76.9 + - + +
570A MET* 4.9 0.2 - - - -
571A ALA* 4.0 14.8 - - + -
573A TYR* 3.9 10.5 - - - -
580A ASP* 4.4 3.4 - - - -
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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
----------------------------------------------------------
534A ILE* 4.4 7.4 - - + -
535A PHE* 1.3 79.1 - - - +
537A ARG* 1.3 66.9 + - - +
542A ASN 3.5 1.4 - - - +
543A GLU* 4.3 2.6 - - - +
544A THR* 2.9 69.1 + - + +
546A VAL* 4.1 12.8 - - + +
555A TYR* 5.4 1.2 + - - -
557A LEU* 3.3 39.1 - - + +
558A SER 4.9 7.4 + - - -
560A LEU* 4.8 13.7 - - + -
566A TYR* 5.0 14.6 - + + -
567A MET 3.1 13.2 - - - +
568A VAL* 3.7 15.0 - - + -
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Residues in contact with ARG 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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536A TYR* 1.3 77.7 - - - +
538A THR* 1.3 71.6 + - - +
541A GLY 4.5 3.1 - - - +
542A ASN 3.3 27.6 - - - +
543A GLU* 3.8 14.8 - - + +
566A TYR* 3.6 8.6 - - - -
567A MET* 2.9 51.0 + - + +
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Residues in contact with THR 538 (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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537A ARG* 1.3 87.9 - - - +
539A ILE* 1.3 79.2 + - + +
540A ILE* 3.0 6.5 + - + +
541A GLY* 3.2 26.0 + - - +
564A THR* 3.8 18.1 - - + +
565A LEU* 3.2 20.9 - - + +
566A TYR* 3.4 20.6 - - - -
567A MET* 4.5 4.1 - - - +
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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