Contacts of the strand formed by residues 596 - 604 (chain I) in PDB entry 5G04
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 TYR 596 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561I ARG* 3.7 36.8 + - + +
589I THR* 3.8 20.9 - - - -
590I ILE 3.8 4.3 - - - -
591I LEU* 3.4 38.5 - - + +
594I SER* 5.4 4.3 - - - -
595I LEU* 1.3 73.3 - - - +
597I LYS* 1.3 61.0 + - - +
636I TYR 4.7 0.7 - - - +
637I SER* 2.9 16.5 + - - +
638I CYS* 3.1 45.2 + - - +
639I LEU* 5.4 7.4 - - + -
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Residues in contact with LYS 597 (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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589I THR* 3.2 4.3 - - - -
590I ILE* 2.9 50.8 + - + +
592I GLU* 3.9 30.0 + - + +
595I LEU* 3.4 13.2 + - + +
596I TYR* 1.3 71.3 - - - +
598I MET* 1.3 65.2 + - - +
599I CYS* 3.7 1.4 + - - -
617I ALA* 4.1 13.7 - - + +
618I ILE 3.9 11.9 - - - +
619I LYS* 4.7 9.9 - - - -
700I ILE 5.3 0.4 + - - -
702I THR* 2.5 45.1 + - - +
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Residues in contact with MET 598 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572I PHE* 5.7 1.1 - - + -
587I LEU* 4.3 9.4 - - + -
588I PHE 3.8 7.0 - - - +
589I THR* 4.1 4.3 - - + -
596I TYR 4.1 1.8 + - - -
597I LYS* 1.3 74.4 - - - +
599I CYS* 1.3 65.7 + - - +
600I ILE* 3.7 26.7 - - + -
617I ALA* 3.2 4.3 - - - +
618I ILE* 2.9 44.3 + - + +
620I PHE* 4.7 8.0 - - + -
638I CYS* 4.0 20.1 - - + +
641I ALA* 3.9 21.5 - - + -
649I VAL* 4.1 18.4 - - + -
651I VAL* 4.2 18.4 - - - -
669I LEU* 3.8 23.3 - - + -
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Residues in contact with CYS 599 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587I LEU* 3.5 4.2 - - - -
588I PHE* 2.8 66.2 + - + -
590I ILE* 3.7 35.7 - - - -
597I LYS* 4.0 2.5 - - - -
598I MET* 1.3 80.3 - - - +
600I ILE* 1.3 66.1 + - - +
615I LEU* 4.2 5.6 - - + -
616I ILE 3.5 7.6 - - - +
617I ALA* 4.1 14.6 - - - -
700I ILE* 4.9 7.2 - - - -
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Residues in contact with ILE 600 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585I TYR* 3.8 22.9 - - + -
586I LEU 3.6 2.5 - - - -
587I LEU* 3.7 24.5 - - + -
598I MET* 3.7 19.3 - - + -
599I CYS* 1.3 75.8 - - - +
601I LEU* 1.3 61.9 + - - +
614I GLY 3.5 3.6 - - - +
615I LEU* 3.5 3.3 - - - +
616I ILE* 2.8 38.7 + - + +
618I ILE* 4.4 17.0 - - + -
643I PHE* 5.3 1.3 - - + -
649I VAL* 5.5 0.4 - - + -
669I LEU* 4.6 3.8 - - + -
671I LEU* 4.4 22.0 - - + -
674I VAL* 4.4 15.3 - - + -
675I TYR* 3.2 24.4 + - + +
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Residues in contact with LEU 601 (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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233I TYR* 4.4 15.3 - - + -
554I ILE* 4.2 22.4 - - + -
556I LEU* 4.8 6.5 - - + -
584I HIS 5.4 0.9 - - - +
585I TYR* 3.4 4.3 - - - -
586I LEU* 2.8 52.3 + - + +
588I PHE* 4.0 13.1 - - + -
600I ILE* 1.3 74.8 - - - +
602I ARG* 1.3 68.4 + - - +
603I ARG* 3.9 24.7 - - + -
614I GLY 3.2 8.3 - - - +
615I LEU* 4.0 6.5 - - + -
689I TYR* 4.7 11.0 - - + -
693I LEU* 4.3 23.1 - - + -
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Residues in contact with ARG 602 (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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583I LEU* 4.0 17.0 - - + +
584I HIS 3.0 12.3 - - - +
585I TYR* 2.7 53.1 + - + -
601I LEU* 1.3 79.8 - - - +
603I ARG* 1.3 68.5 + - - +
611I VAL* 3.6 18.9 - - + +
612I SER* 2.7 45.9 + - - -
613I ASN* 3.5 23.7 + - - +
614I GLY* 2.9 18.5 + - - -
675I TYR* 3.7 32.0 - - - +
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Residues in contact with ARG 603 (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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233I TYR* 3.9 9.2 - - - +
235I GLN* 3.5 37.6 + - - +
552I ILE* 4.2 20.2 - - - +
554I ILE* 3.8 28.0 - - - +
583I LEU* 3.5 4.2 - - - +
584I HIS* 2.9 33.0 + - + +
601I LEU* 3.9 14.8 - - + -
602I ARG* 1.3 79.6 - - - +
604I HIS* 1.3 66.3 + - - +
607I ILE 4.1 16.6 + - - -
609I GLN 4.8 10.4 + - - -
610I SER* 5.3 7.2 - - - +
611I VAL* 4.0 8.3 - - - -
689I TYR* 6.1 6.5 - - - -
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Residues in contact with HIS 604 (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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235I GLN* 3.6 13.7 + - - +
581I SER 4.6 3.1 + - - -
582I ASN* 3.5 20.8 + - + -
583I LEU* 3.5 21.3 - - + +
584I HIS* 5.3 0.4 - - - -
603I ARG* 1.3 79.0 + - - +
605I THR* 1.3 81.9 + - + +
606I ASP* 3.1 22.2 + - + +
609I GLN* 3.3 34.5 + - + +
610I SER* 3.9 16.5 - - - +
611I VAL* 4.0 11.0 - - + +
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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