Contacts of the strand formed by residues 603 - 612 (chain I) in PDB entry 3RWR
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 ALA 603 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545I TRP* 4.1 2.0 - - - +
599I CYS* 2.8 20.9 - - - -
600I VAL 3.2 16.0 + - - +
601I ALA 3.0 3.4 - - - +
602I ASP* 1.3 79.2 - - - +
604I LEU* 1.3 61.3 + - - +
623I CYS 3.6 7.6 - - - +
624I MET* 3.3 22.4 - - + +
600W VAL* 4.7 6.4 - - - +
601W ALA* 4.9 7.4 - - + -
602W ASP* 5.2 2.5 - - + +
603W ALA* 3.9 22.4 - - + +
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Residues in contact with LEU 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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523I LEU* 4.0 14.4 - - + -
538I VAL* 4.0 19.5 - - + -
545I TRP* 3.1 55.7 - - + +
597I CYS* 4.2 6.7 - - - -
599I CYS* 3.4 17.5 - - + -
603I ALA* 1.3 73.2 - - - +
605I ILE* 1.3 64.0 + - - +
606I LEU* 4.3 10.1 - - + +
622I HIS 4.9 0.2 - - - -
623I CYS* 2.6 69.8 + - + +
601W ALA* 5.3 1.3 - - - -
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Residues in contact with ILE 605 (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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597I CYS* 3.2 11.7 - - - -
598I ASP* 2.7 37.5 + - - +
599I CYS* 4.2 0.8 - - - +
603I ALA 4.4 0.2 - - - -
604I LEU* 1.3 72.8 - - - +
606I LEU* 1.3 62.4 + - - +
607I ARG* 3.3 30.9 + - - +
620I ASN* 3.2 34.1 - - + +
621I PHE 3.4 3.8 - - - +
622I HIS* 3.4 32.3 - - + +
623I CYS 4.4 0.4 - - - +
600W VAL* 4.7 6.5 - - + -
601W ALA* 4.0 23.5 - - + +
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Residues in contact with LEU 606 (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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516I LEU* 5.6 3.1 - - + -
518I LEU* 4.8 3.4 - - + -
523I LEU* 4.2 14.8 - - + -
536I LEU* 4.4 8.5 - - + -
538I VAL* 4.6 9.6 - - + -
595I PHE* 3.4 38.1 - - + -
597I CYS* 3.5 28.5 - - + -
604I LEU* 4.3 9.4 - - + +
605I ILE* 1.3 69.7 - - - +
607I ARG* 1.3 62.5 + - - +
608I VAL* 3.0 23.8 + - + +
620I ASN* 3.2 3.9 - - - -
621I PHE* 3.0 53.0 + - + +
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Residues in contact with ARG 607 (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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595I PHE* 3.2 27.5 - - - +
596I SER* 2.9 27.5 + - - +
597I CYS* 3.8 4.0 - - - +
598I ASP* 2.8 44.7 + - - +
605I ILE* 3.3 33.1 + - - +
606I LEU* 1.3 70.8 - - - +
608I VAL* 1.3 60.3 + - - +
609I ARG* 3.9 6.8 + - + +
620I ASN* 3.1 25.5 + - - +
600W VAL* 4.6 4.8 - - - +
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Residues in contact with VAL 608 (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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576I LEU* 5.4 5.8 - - + -
579I LEU* 5.7 5.8 - - + -
580I LEU* 5.0 5.4 - - + -
595I PHE* 3.9 27.4 - - + +
606I LEU* 3.3 33.4 - - + +
607I ARG* 1.3 70.8 - - - +
609I ARG* 1.3 71.3 + - - +
610I SER* 5.0 5.4 - - - -
617I PHE 4.1 0.3 - - - +
618I TYR* 3.9 3.8 - - - -
619I TRP* 2.8 52.9 + - + +
620I ASN* 3.2 1.7 + - - +
621I PHE* 3.7 22.2 - - + -
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Residues in contact with ARG 609 (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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593I ALA* 2.9 24.7 - - - +
594I THR* 3.2 41.4 + - + +
595I PHE* 3.8 7.5 + - - +
596I SER* 5.1 4.0 - - - +
607I ARG* 5.1 8.1 - - + +
608I VAL* 1.3 81.7 - - - +
610I SER* 1.3 91.4 + - - +
611I GLU* 5.3 5.7 + - - +
616I PRO* 5.2 4.8 - - - +
617I PHE 3.6 7.0 + - - -
618I TYR* 3.4 51.4 + - - -
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Residues in contact with SER 610 (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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579I LEU* 3.1 44.2 - - - +
589I HIS* 4.4 3.5 - - - -
592I GLU 3.1 20.1 + - - -
593I ALA* 4.4 3.9 - - - +
608I VAL* 5.0 4.5 - - - -
609I ARG* 1.3 86.5 + - - +
611I GLU* 1.3 76.8 + - - +
617I PHE* 2.8 31.1 + - - +
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Residues in contact with GLU 611 (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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65F LYS* 3.1 23.0 + - - -
579I LEU* 3.4 8.8 - - - +
592I GLU* 3.3 37.1 + - + +
609I ARG* 5.3 5.8 + - - +
610I SER* 1.3 92.2 + - - +
612I LEU* 1.3 77.3 + - - +
614I GLY* 3.0 32.0 - - - +
615I LEU 3.6 6.5 - - - +
616I PRO* 3.8 15.2 - - + +
617I PHE* 3.8 3.8 - - - +
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Residues in contact with LEU 612 (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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101F LEU* 5.8 2.9 - - + -
104F VAL* 6.0 4.0 - - + -
106F PHE* 5.7 9.0 - - + -
575I HIS* 3.1 54.5 - - + +
578I ASN* 5.2 4.5 - - + +
579I LEU* 3.4 18.8 - - + -
611I GLU* 1.3 82.4 - - - +
613I SER* 1.3 64.8 + - - +
614I GLY 2.8 9.8 + - - -
615I LEU* 2.8 30.0 + - + +
617I PHE* 3.3 35.4 - - + -
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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