Contacts of the strand formed by residues 597 - 606 (chain A) in PDB entry 4X61
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 THR 597 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A GLU* 3.8 28.0 - - + +
540A PHE 3.4 25.9 + - - +
541A PRO* 4.7 6.7 - - + +
595A GLY 4.7 2.6 + - - -
596A GLN* 1.3 77.0 + - - +
598A ILE* 1.3 66.4 + - - +
599A CYS* 4.6 1.3 - - + +
619A ALA* 3.5 23.3 - - + +
620A PRO* 3.6 7.2 - - - +
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Residues in contact with ILE 598 (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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474A PRO* 3.9 19.1 - - + -
512A LEU* 4.4 5.8 - - + -
538A LEU 3.8 1.0 - - - +
539A GLU* 3.6 1.2 - - - -
540A PHE* 2.7 47.1 + - + +
542A VAL* 3.6 24.9 - - + -
548A LEU* 4.1 18.8 - - + -
551A PHE* 3.8 32.5 - - + -
592A VAL* 3.8 31.0 - - + -
596A GLN 4.2 0.2 + - - -
597A THR* 1.3 72.7 - - - +
599A CYS* 1.3 64.6 + - - +
617A VAL* 4.6 1.8 - - + -
619A ALA 3.3 8.3 - - - +
620A PRO* 4.3 4.0 - - + -
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Residues in contact with CYS 599 (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 THR* 3.7 24.7 - - - -
538A LEU 3.2 13.0 - - - +
539A GLU* 4.5 17.5 - - - +
597A THR* 3.7 2.5 + - + +
598A ILE* 1.3 73.5 - - - +
600A VAL* 1.3 61.8 + - - +
601A ARG* 3.9 7.4 - - - -
617A VAL* 3.4 5.4 - - - +
618A THR* 2.8 53.2 + - - +
619A ALA* 2.9 26.0 + - + -
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Residues in contact with VAL 600 (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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472A LEU* 4.7 1.3 - - + -
536A CYS 4.0 0.3 - - - +
537A THR* 3.6 3.5 - - - +
538A LEU* 2.9 47.1 + - + +
540A PHE* 3.8 18.4 - - + -
551A PHE* 3.5 45.8 - - + -
598A ILE 4.1 0.6 - - - -
599A CYS* 1.3 76.4 - - - +
601A ARG* 1.3 66.2 + - - +
602A PHE* 3.7 30.3 - - + -
615A TRP* 5.0 1.6 - - + -
616A ALA 3.4 15.7 - - - +
617A VAL* 4.5 0.7 - - + -
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Residues in contact with ARG 601 (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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535A TYR* 3.2 28.2 + - + -
536A CYS 3.4 5.4 - - - -
537A THR* 3.5 35.3 + - - +
599A CYS* 4.4 4.2 - - - -
600A VAL* 1.3 76.6 - - - +
602A PHE* 1.3 63.3 + - - +
603A TRP* 3.7 25.5 - - + -
615A TRP* 3.2 7.6 - - - +
616A ALA* 2.8 31.7 + - + +
618A THR* 3.2 47.0 + - + +
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Residues in contact with PHE 602 (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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440A PHE* 4.7 7.9 - + - -
472A LEU* 3.5 30.7 - - + -
518A CYS* 4.1 10.1 - - - -
519A PHE* 3.4 16.9 - - + -
535A TYR* 3.4 1.6 - - - -
536A CYS* 3.0 34.7 + - - +
551A PHE* 4.7 6.1 - + + -
584A PHE* 3.5 58.1 - + + -
600A VAL* 3.7 20.6 - - + -
601A ARG* 1.3 79.0 - - - +
603A TRP* 1.3 62.3 + - - +
613A TYR* 4.7 11.9 - + + -
614A GLU 3.5 4.9 - - - -
615A TRP* 3.6 28.5 - + + -
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Residues in contact with TRP 603 (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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519A PHE* 4.1 3.6 - - - -
534A ARG 3.4 6.1 - - - +
535A TYR* 3.0 55.5 - + + -
601A ARG* 3.7 33.0 - - + -
602A PHE* 1.3 75.4 - - - +
604A ARG* 1.3 59.7 + - - +
605A CYS* 3.8 19.1 - - - -
613A TYR* 3.2 9.7 - - - +
614A GLU* 2.7 68.0 + - + +
615A TRP 3.9 3.8 - - - -
616A ALA* 3.9 21.3 - - + -
625A ILE* 4.8 15.0 - - + -
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Residues in contact with ARG 604 (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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442A ASP* 2.5 45.5 + - - -
445A LEU* 3.8 8.1 - - - +
447A PRO* 3.9 6.2 - - - +
448A GLU* 2.7 44.4 + - - -
519A PHE* 3.8 16.6 - - + -
521A PHE* 3.7 15.7 - - - -
532A ASN* 3.2 29.9 + - - +
533A ASN* 3.5 11.0 + - - +
534A ARG* 2.9 37.3 + - + +
603A TRP* 1.3 73.8 - - - +
605A CYS* 1.3 64.6 + - - +
606A SER* 5.6 1.2 - - - -
611A VAL* 3.8 14.5 - - + +
612A TRP 3.8 3.8 - - - +
613A TYR* 3.7 18.0 - - + -
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Residues in contact with CYS 605 (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 ASN* 3.7 4.3 - - - -
603A TRP* 3.8 17.9 - - - -
604A ARG* 1.3 80.4 - - - +
606A SER* 1.3 65.5 + - - +
611A VAL* 3.3 6.9 - - - +
612A TRP* 2.7 58.6 + - + +
614A GLU* 3.5 34.8 - - - -
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Residues in contact with SER 606 (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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448A GLU* 5.2 4.1 + - - -
532A ASN* 5.6 1.9 - - - +
533A ASN* 2.6 33.4 + - - -
604A ARG* 5.6 1.1 - - - -
605A CYS* 1.3 79.1 - - - +
607A ASN* 1.3 65.1 + - - +
610A LYS 3.3 13.9 - - - -
611A VAL* 3.8 16.8 - - - -
612A TRP* 3.7 9.1 - - - -
637A LEU* 5.5 0.4 - - - -
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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