Contacts of the strand formed by residues 536 - 548 (chain A) in PDB entry 2C11
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 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A VAL 4.4 0.2 - - - +
534A GLY* 3.4 5.4 - - - +
535A LEU* 1.3 96.2 + - - +
537A ASN* 1.3 69.4 + - - +
538A TRP* 3.8 14.9 - - + -
591A SER* 3.6 15.8 + - - -
592A ASN* 4.1 2.7 + - + -
593A HIS* 6.4 1.8 - - + +
671A GLY* 3.5 28.5 - - - +
672A LYS* 3.2 8.4 - - - -
673A ASP 4.9 0.3 + - - -
1F NAG 4.2 27.1 - - - +
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Residues in contact with ASN 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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530A LEU 3.8 7.1 - - - +
531A ASP* 3.6 7.3 - - - -
532A VAL* 3.0 56.4 + - - +
534A GLY 3.5 3.5 + - - +
535A LEU 3.2 11.4 - - - +
536A GLU* 1.3 84.2 + - - +
538A TRP* 1.3 64.0 + - - +
589A LEU* 4.5 14.7 - - + +
590A ALA 2.8 12.3 + - - +
671A GLY 3.4 13.9 + - - -
672A LYS 2.8 8.0 + - - +
674A LEU* 3.0 29.2 + - + +
1736A CA 3.9 2.4 - - - -
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Residues in contact with TRP 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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536A GLU* 3.8 12.8 - - + -
537A ASN* 1.3 77.7 - - - +
539A VAL* 1.3 65.2 + - - +
540A TRP* 4.0 14.5 + + - +
568A LEU* 3.9 29.9 - - + +
569A LEU 5.4 0.4 - - - -
588A TYR 3.7 0.3 - - - +
589A LEU* 3.0 7.4 - - - +
590A ALA 2.6 28.9 + - - +
591A SER 3.7 15.5 - - - -
592A ASN* 3.2 55.2 - - + -
669A ILE 4.1 3.6 - - - -
670A ALA* 3.1 31.8 - - + +
671A GLY* 3.0 31.4 - - - +
674A LEU* 4.5 0.4 - - - -
1F NAG 4.1 6.1 - - - -
2F FUC 4.6 8.5 - - - -
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Residues in contact with VAL 539 (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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538A TRP* 1.3 78.9 - - - +
540A TRP* 1.3 62.2 + - - +
568A LEU* 2.9 11.1 - - - +
569A LEU* 2.9 61.0 + - + +
575A ALA* 4.7 4.5 - - + -
587A LEU* 3.4 19.7 - - + -
588A TYR 3.5 3.6 - - - +
589A LEU* 3.8 19.3 - - + -
634A VAL* 4.3 9.9 - - + -
669A ILE* 3.9 24.0 - - + +
674A LEU* 4.1 13.0 - - + -
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Residues in contact with TRP 540 (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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538A TRP* 4.1 13.0 - + + +
539A VAL* 1.3 76.8 - - - +
541A ALA* 1.3 58.4 + - - +
542A GLU* 4.0 3.1 - - + -
566A ARG* 4.0 29.6 - - + -
567A LYS 3.9 9.9 - - - -
568A LEU* 3.5 46.7 - - + -
586A TYR 3.8 0.6 - - - +
587A LEU* 2.8 27.6 - - - +
588A TYR* 2.9 63.0 + + + +
590A ALA* 3.5 21.4 - - + +
591A SER 5.1 1.4 + - - -
600A PRO* 4.4 18.7 - - + +
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Residues in contact with ALA 541 (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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540A TRP* 1.3 73.2 - - - +
542A GLU* 1.3 63.0 + - - +
543A ASP* 4.2 0.6 + - - +
565A THR* 3.3 3.8 + - - +
567A LYS* 3.0 41.5 + - + +
569A LEU* 4.2 19.5 - - + -
577A PHE* 5.9 0.4 - - + -
584A PRO* 3.5 30.7 - - + -
586A TYR 3.6 4.0 - - - -
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Residues in contact with GLU 542 (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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540A TRP* 4.6 0.2 - - + -
541A ALA* 1.3 78.0 - - - +
543A ASP* 1.3 65.6 + - - +
564A VAL* 5.1 5.8 - - + +
565A THR 2.9 8.5 - - - +
566A ARG* 2.7 42.5 + - + -
584A PRO* 4.1 0.5 - - - +
585A ARG 3.9 1.6 + - - -
586A TYR* 2.8 43.6 + - + +
588A TYR* 2.3 45.6 + - + +
708A TYR* 2.9 21.3 + - - -
509B ASN* 4.7 0.7 - - - +
685B ILE* 3.7 15.0 - - + +
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Residues in contact with ASP 543 (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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541A ALA 5.3 0.2 - - - -
542A GLU* 1.3 75.8 - - - +
544A MET* 1.3 79.9 + - - +
564A VAL* 4.3 3.4 - - - -
565A THR* 2.6 50.4 + - - +
583A THR 4.0 3.1 - - - +
584A PRO* 3.6 11.3 - - + +
585A ARG* 2.8 63.8 + - - +
683B LEU* 4.6 7.9 - - - -
685B ILE* 4.8 1.4 - - - +
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Residues in contact with MET 544 (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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543A ASP* 1.3 97.4 + - - +
545A VAL* 1.3 70.1 + - - +
546A PHE* 4.1 11.9 - - + -
562A LEU* 4.2 17.3 - - + -
563A GLN 3.3 11.9 - - - +
564A VAL* 4.4 1.8 - - - +
565A THR* 4.2 3.1 - - - +
585A ARG* 3.7 9.2 - - - +
519B VAL* 5.6 0.9 - - + -
521B THR* 4.2 4.9 - - + -
612B GLY* 3.5 14.1 - - - -
613B GLU* 3.1 67.1 - - + +
683B LEU* 4.0 30.7 - - + +
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Residues in contact with VAL 545 (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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544A MET* 1.3 83.1 - - - +
546A PHE* 1.3 72.8 + - - +
547A VAL* 4.2 10.3 - - + -
561A ARG 3.6 1.0 - - - +
562A LEU* 3.6 3.9 - - - +
563A GLN* 2.9 49.6 + - + +
565A THR* 3.8 19.7 - - + -
613B GLU* 4.3 10.1 - - - +
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Residues in contact with PHE 546 (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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544A MET* 4.1 8.5 - - + -
545A VAL* 1.3 79.8 - - - +
547A VAL* 1.3 62.3 + - - +
548A PRO* 3.7 8.8 - - - +
560A GLN* 3.8 21.7 - - + +
561A ARG 3.7 0.4 - - - -
562A LEU* 3.1 38.4 - - + -
371B ILE* 4.2 12.3 - - + -
521B THR* 5.7 1.1 - - + -
613B GLU* 3.1 34.4 + - + -
614B PRO 3.3 4.3 - - - -
615B LEU* 3.3 42.6 - - + -
616B PRO* 3.1 34.1 - - + +
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Residues in contact with VAL 547 (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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545A VAL* 4.2 14.6 - - + -
546A PHE* 1.3 74.8 - - - +
548A PRO* 1.3 67.6 - - + +
549A MET* 3.3 21.6 - - + +
560A GLN* 4.4 0.7 - - - -
561A ARG* 2.6 45.5 + - - +
563A GLN* 3.4 34.8 - - + +
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Residues in contact with PRO 548 (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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546A PHE 3.7 8.5 - - - +
547A VAL* 1.3 91.9 - - + +
549A MET* 1.3 60.4 + - - +
558A GLN* 3.4 15.9 - - + +
559A LEU 2.9 8.3 - - - +
560A GLN* 3.6 22.2 - - - +
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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