Contacts of the strand formed by residues 415 - 424 (chain R) in PDB entry 1G4W
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 ILE 415 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409R ALA 3.8 1.7 - - - +
410R SER* 3.4 20.6 - - - +
412R GLY* 3.7 7.9 + - - +
414R ALA* 1.3 91.9 - - + +
416R ASP* 1.3 80.6 + - - +
417R GLN 4.4 0.4 - - - +
434R LEU* 4.0 19.5 - - + -
435R HIS 3.5 13.0 - - - +
436R VAL* 4.9 8.7 - - + -
437R LYS* 5.7 0.2 - - - -
438R ASN* 5.2 0.7 - - - +
453R TYR* 3.7 26.9 - - + -
454R LEU* 4.7 19.3 - - + -
457R ARG* 3.5 38.8 - - + +
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Residues in contact with ASP 416 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391R ARG* 5.3 0.3 + - - -
405R LYS* 4.2 19.4 + - - -
410R SER* 3.5 20.4 - - - +
412R GLY 5.0 1.0 - - - +
415R ILE* 1.3 81.6 - - - +
417R GLN* 1.3 60.6 + - - +
418R TYR* 3.8 23.9 + - + +
433R VAL 3.9 0.3 - - - +
434R LEU 3.8 0.2 - - - -
435R HIS* 2.8 42.5 + - + +
437R LYS* 3.1 36.2 + - - +
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Residues in contact with GLN 417 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405R LYS* 3.7 2.1 - - - -
406R VAL* 2.8 34.3 + - + +
409R ALA* 3.5 20.3 - - + +
410R SER* 2.8 14.7 + - - +
415R ILE 4.1 0.8 - - - -
416R ASP* 1.3 73.1 - - - +
418R TYR* 1.3 71.0 + - - +
419R ASN* 5.3 2.8 + - - -
432R PRO* 4.7 11.7 - - + +
433R VAL 3.1 13.5 - - - +
434R LEU* 3.6 17.3 - - + +
457R ARG* 2.5 41.1 - - - +
461R SER* 5.3 7.4 - - - -
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Residues in contact with TYR 418 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390R PHE* 3.8 20.6 - + - -
391R ARG* 3.5 43.4 + - + +
403R SER* 3.2 26.2 - - - +
404R GLN 3.5 6.3 - - - +
405R LYS* 3.5 47.1 + - + -
406R VAL* 3.9 4.5 - - - -
416R ASP* 3.8 31.0 + - + +
417R GLN* 1.3 83.3 - - - +
419R ASN* 1.3 64.0 + - - +
432R PRO* 3.6 4.2 - - - +
433R VAL* 2.9 46.7 + - + +
435R HIS* 4.3 2.9 + - + -
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Residues in contact with ASN 419 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402R ASN 3.7 2.1 - - - +
403R SER* 3.4 2.5 - - - -
404R GLN* 3.1 44.0 + - + +
406R VAL* 4.2 12.6 - - + +
417R GLN* 5.3 3.2 + - - -
418R TYR* 1.3 80.8 + - - +
420R MET* 1.3 61.0 + - - +
421R GLN* 3.8 8.2 + - - +
430R THR* 2.9 28.8 - - - +
431R ILE 4.3 0.9 - - - -
432R PRO* 4.3 14.5 - - - +
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Residues in contact with MET 420 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361R MET* 3.7 21.8 - - + -
364R LEU* 4.7 3.4 - - - -
372R LEU* 4.2 11.0 - - + -
389R TYR* 4.1 6.1 - - + +
390R PHE* 3.2 49.4 - - + +
401R THR* 3.4 18.4 - - - +
402R ASN 3.6 2.7 - - - -
403R SER* 4.0 8.1 - - - +
418R TYR 4.0 0.4 - - - -
419R ASN* 1.3 71.8 - - - +
421R GLN* 1.3 60.1 + - - +
422R LEU* 3.7 9.4 + - + -
429R TYR 3.5 2.3 - - - +
430R THR* 3.1 4.1 - - - -
431R ILE* 2.9 55.7 + - + +
433R VAL* 3.7 15.9 - - + -
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Residues in contact with GLN 421 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400R HIS* 3.8 1.9 - - - +
401R THR* 3.4 2.3 - - - -
402R ASN* 2.8 58.2 + - + +
404R GLN* 4.2 25.7 + - - +
419R ASN* 4.8 7.3 + - - +
420R MET* 1.3 72.9 - - - +
422R LEU* 1.3 62.0 + - - +
423R SER* 4.1 4.8 + - - +
429R TYR 3.8 4.3 - - - -
430R THR* 3.2 24.2 - - + +
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Residues in contact with LEU 422 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361R MET* 3.3 42.0 - - + +
364R LEU* 3.7 31.2 - - + -
365R LEU* 3.8 28.5 - - + +
399R VAL* 4.7 3.8 - - + -
400R HIS 3.3 4.3 - - - +
401R THR* 3.5 16.6 - - - +
420R MET* 3.8 12.8 - - + +
421R GLN* 1.3 74.2 - - - +
423R SER* 1.3 62.1 + - - +
428R ARG* 3.3 5.4 - - - +
429R TYR* 2.8 41.4 + - + +
431R ILE* 4.2 13.2 - - + -
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Residues in contact with SER 423 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365R LEU* 4.7 0.7 - - - -
398R GLU 3.8 0.5 - - - +
399R VAL* 3.3 3.3 - - - +
400R HIS* 2.7 54.6 + - - +
421R GLN* 4.7 5.4 + - - +
422R LEU* 1.3 76.8 + - - +
424R CYS* 1.3 63.6 + - - +
427R LYS 3.5 6.1 - - - -
428R ARG* 3.7 25.0 + - - -
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Residues in contact with CYS 424 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362R LYS* 4.5 9.9 - - - -
365R LEU* 4.2 20.4 - - + +
398R GLU* 3.6 29.4 - - - +
399R VAL* 4.0 19.3 - - + -
423R SER* 1.3 76.9 - - - +
425R GLY* 1.3 66.7 + - - +
426R GLU 3.3 0.3 + - - -
427R LYS* 2.9 34.0 + - + +
428R ARG* 4.0 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