Contacts of the strand formed by residues 518 - 523 (chain G) 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 HIS 518 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507G ARG* 3.9 0.3 - - - -
508G ILE* 2.8 35.5 + - + +
510G LEU* 3.6 35.2 - - + +
513G GLU* 4.9 5.1 + - + -
516G ILE* 2.6 56.4 + - + +
517G THR* 1.3 73.7 - - - +
519G PHE* 1.3 75.6 + - - +
536G LEU* 3.4 30.3 - - + -
537G THR 3.2 15.0 - - - +
538G ASP* 3.6 16.3 + - + +
543G TRP* 5.6 2.0 - + - -
588G PHE* 4.6 1.8 - + - -
590G LYS* 4.4 13.1 + - - -
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Residues in contact with PHE 519 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ARG* 4.1 20.4 - - + -
127F ILE* 3.3 53.2 - - + -
128F CYS* 3.7 21.8 - - + -
131F LEU* 4.3 12.1 - - + -
505G ILE* 4.3 6.5 - - + -
506G SER 4.0 1.8 - - - -
507G ARG* 4.0 26.7 - - + -
517G THR* 3.8 14.1 - - - -
518G HIS* 1.3 91.1 - - - +
520G LEU* 1.3 64.1 + - - +
521G GLN* 3.5 3.6 + - - +
535G THR 3.6 0.9 - - - +
536G LEU* 3.4 14.2 - - - +
537G THR* 2.8 33.5 + - + +
538G ASP* 5.3 0.7 - - - -
539G GLY 5.3 0.4 - - - -
626G LEU* 4.0 17.6 - - + +
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Residues in contact with LEU 520 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504G LYS 4.1 0.7 - - - +
505G ILE* 3.5 1.1 - - - -
506G SER* 2.7 48.4 + - - +
508G ILE* 3.7 17.1 - - + +
519G PHE* 1.3 71.9 - - - +
521G GLN* 1.3 60.9 + - - +
522G VAL* 3.2 34.3 - - + +
534G ILE* 3.8 13.5 - - + -
535G THR 3.9 2.9 - - - +
536G LEU* 3.6 7.9 - - + +
574G LEU* 4.0 11.7 - - + +
586G PHE* 3.5 26.5 - - + -
595G PHE* 3.5 38.4 - - + -
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Residues in contact with GLN 521 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503G ARG* 3.6 52.0 + - + +
504G LYS 4.7 0.7 - - - +
505G ILE* 3.5 33.1 - - + +
519G PHE 4.6 3.1 - - - +
520G LEU* 1.3 74.6 - - - +
522G VAL* 1.3 63.4 + - - +
523G SER* 3.7 8.1 + - - +
533G VAL 3.9 0.2 - - - +
534G ILE* 3.7 2.4 - - - -
535G THR* 2.8 51.5 + - - +
537G THR* 6.4 0.2 - - + -
625G GLU* 4.4 7.7 + - - -
626G LEU* 4.2 19.0 - - + +
629G TYR* 5.3 0.5 - - - -
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Residues in contact with VAL 522 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503G ARG* 4.3 1.3 - - - -
504G LYS* 3.4 28.0 + - - +
520G LEU* 3.2 25.5 - - + +
521G GLN* 1.3 70.7 - - - +
523G SER* 1.3 61.3 + - - +
524G TRP* 3.4 24.4 - - + +
532G PHE* 4.1 35.7 - - + -
533G VAL 3.9 5.8 - - - +
534G ILE* 4.5 9.0 - - + +
574G LEU* 4.1 27.8 - - + +
575G LEU* 4.6 12.3 - - + -
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Residues in contact with SER 523 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501G MET* 3.0 38.8 - - - +
502G GLU 3.9 5.4 - - - -
503G ARG* 4.0 13.9 - - - +
521G GLN* 3.7 9.2 + - - -
522G VAL* 1.3 71.0 - - - +
524G TRP* 1.3 59.8 + - - +
531G GLY 5.0 0.2 - - - +
533G VAL* 2.8 53.7 + - - +
535G THR* 5.7 1.0 + - - -
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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