Contacts of the strand formed by residues 587 - 594 (chain I) in PDB entry 6C6U
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 587 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149I LEU* 5.5 0.7 - - + -
448I LEU* 4.3 20.7 + - + +
451I ARG 5.2 2.4 + - - +
453I ILE* 3.6 34.3 - - + -
557I ARG* 3.6 43.1 + - + +
558I VAL* 3.8 20.6 - - + -
575I LEU* 3.9 17.9 - - + -
579I ALA* 4.7 4.5 - - + -
580I GLN 3.3 18.8 - - - +
581I THR* 4.3 3.8 - - - +
582I ASN* 5.0 0.2 - - - -
586I PHE* 1.3 79.8 - - - +
588I GLU* 1.3 62.1 + - - +
607I SER* 3.5 17.8 - - - -
608I ALA* 3.7 4.2 + - - +
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Residues in contact with GLU 588 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557I ARG* 4.6 3.4 - - - +
579I ALA* 3.6 4.2 - - - +
580I GLN* 3.1 53.9 + - + +
581I THR 3.6 10.0 - - - +
582I ASN* 2.9 41.7 + - + +
587I LEU* 1.3 76.4 - - - +
589I THR* 1.3 62.7 + - - +
605I TYR* 4.1 24.9 - - + +
606I LEU 3.1 19.4 - - - +
607I SER* 4.2 2.4 + - - -
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Residues in contact with THR 589 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555I TYR 4.8 0.9 - - - +
556I GLY* 3.3 29.0 + - - +
557I ARG* 4.0 19.1 - - + +
578I TYR* 4.7 1.5 - - - +
579I ALA* 5.1 0.4 - - - -
588I GLU* 1.3 75.8 - - - +
590I PRO* 1.3 80.0 + - - +
591I TYR* 3.6 30.9 - - + +
605I TYR* 3.5 4.8 - - - -
606I LEU 2.9 30.7 + - - +
659I GLN* 3.8 12.5 + - - -
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Residues in contact with PRO 590 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I LEU* 3.9 22.9 - - + -
578I TYR* 3.6 33.2 - - + +
589I THR* 1.3 98.6 + - - +
591I TYR* 1.3 73.9 + - - +
603I ILE* 4.7 6.5 - - + -
604I HIS 3.8 5.4 - - - +
605I TYR* 3.5 24.7 - - + +
655I VAL* 3.6 20.0 - - + +
659I GLN* 3.9 9.8 - - - +
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Residues in contact with TYR 591 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555I TYR* 4.2 5.2 + - - -
556I GLY* 5.9 0.2 - - - -
589I THR* 3.6 29.2 - - + +
590I PRO* 1.3 82.6 - - - +
592I ARG* 1.3 64.6 + - - +
593I LYS 4.1 0.2 - - - -
603I ILE* 3.3 8.5 - - - +
604I HIS* 2.9 33.4 + - - +
606I LEU* 3.6 40.2 - - + -
611I GLU* 2.6 34.7 + - + -
616I ILE* 3.7 16.8 - - + -
637I ARG* 3.2 4.6 + - - -
652I TYR* 3.7 22.2 - - + -
653I MET 3.5 11.4 - - - +
654I ASP* 3.1 28.9 - - - -
655I VAL* 4.0 3.6 - - - -
659I GLN* 4.3 5.5 + - - -
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Residues in contact with ARG 592 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I PRO 4.8 8.9 + - - -
21I VAL* 3.8 31.5 - - + +
591I TYR* 1.3 76.5 - - - +
593I LYS* 1.3 60.1 + - - +
594I VAL* 3.0 7.3 + - - +
599I VAL* 3.6 37.4 + - + +
600I THR 3.9 11.4 + - - +
601I ASP* 4.5 14.7 - - - +
602I GLU 3.5 9.9 - - - +
603I ILE* 5.2 1.1 - - + -
623I LEU* 5.5 6.9 - - - +
652I TYR* 3.3 5.6 - - - -
653I MET* 2.9 46.9 + - + +
654I ASP 3.6 17.4 + - - -
655I VAL* 3.9 23.8 + - + +
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Residues in contact with LYS 593 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591I TYR 4.1 1.0 + - - -
592I ARG* 1.3 66.7 - - - +
594I VAL* 1.3 62.2 + - - +
595I THR* 3.1 26.3 + - + +
600I THR* 3.3 23.8 + - - -
602I GLU* 3.6 36.7 + - + +
604I HIS* 5.0 10.7 - - + +
614I TYR* 5.1 9.5 - - - -
651I ASP* 4.0 14.7 + - - +
652I TYR* 3.8 41.6 + - + +
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Residues in contact with VAL 594 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592I ARG 3.0 12.6 + - - +
593I LYS* 1.3 72.1 - - - +
595I THR* 1.3 74.7 + - - +
596I ASP* 4.7 1.5 - - - +
597I GLY 4.9 2.2 - - - +
598I VAL 3.8 9.0 - - - +
599I VAL* 3.8 17.0 - - + +
629I PHE* 3.8 28.3 - - + -
648I ASP* 6.0 0.4 - - - +
650I VAL* 3.7 23.3 - - + +
651I ASP* 3.2 23.9 + - - +
652I TYR 3.7 4.9 - - - +
653I MET* 3.6 28.0 - - + +
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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