Contacts of the strand formed by residues 399 - 405 (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 VAL 399 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358R GLU* 4.5 1.8 - - + +
361R MET* 3.7 30.3 - - + +
362R LYS* 3.5 39.9 - - + +
365R LEU* 5.7 2.2 - - + -
394R TYR 4.3 0.2 - - - +
395R THR* 3.7 3.7 - - - +
396R PHE* 2.9 36.9 + - + +
397R GLY 3.2 1.2 - - - -
398R GLU* 1.3 84.8 - - - +
400R HIS* 1.3 71.6 + - - +
422R LEU* 4.7 8.5 - - + -
423R SER 3.3 12.1 - - - +
424R CYS* 4.0 15.9 - - + -
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Residues in contact with HIS 400 (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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393R SER* 4.4 10.8 + - - -
394R TYR 3.3 17.5 + - - -
395R THR* 3.1 25.6 + - + +
398R GLU 4.2 0.4 + - - -
399R VAL* 1.3 79.0 - - - +
401R THR* 1.3 85.9 + - - +
402R ASN* 4.1 12.7 - - + +
421R GLN 3.8 1.3 - - - +
422R LEU* 3.3 5.0 - - - -
423R SER* 2.7 51.0 + - - +
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Residues in contact with THR 401 (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* 3.4 22.4 - - + +
389R TYR 4.3 3.9 + - - +
392R GLY 4.7 1.5 + - - +
393R SER* 3.2 4.2 - - - -
394R TYR* 3.0 54.4 + - + +
396R PHE* 4.0 15.7 - - + -
400R HIS* 1.3 82.1 + - - +
402R ASN* 1.3 63.7 + - - +
403R SER 4.2 1.1 + - - -
420R MET* 3.4 28.2 - - - +
421R GLN 3.4 3.8 - - - -
422R LEU* 3.7 2.9 - - - -
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Residues in contact with ASN 402 (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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392R GLY 3.7 2.6 - - - +
393R SER* 2.8 23.1 + - - -
400R HIS* 4.1 13.9 - - + +
401R THR* 1.3 76.2 + - - +
403R SER* 1.3 63.9 + - - +
404R GLN* 4.1 13.8 + - - +
419R ASN 3.7 2.3 - - - +
420R MET* 3.6 0.3 - - - -
421R GLN* 2.8 58.7 + - + +
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Residues in contact with SER 403 (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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389R TYR 5.4 0.2 - - - -
390R PHE 2.5 33.1 + - - -
391R ARG 2.4 29.9 - - - +
392R GLY* 3.1 11.7 + - - +
401R THR* 4.9 0.9 - - - -
402R ASN* 1.3 77.6 - - - +
404R GLN* 1.3 57.4 + - - +
405R LYS 4.1 1.0 + - - -
418R TYR* 3.2 21.7 - - - +
419R ASN 3.4 7.1 - - - -
420R MET* 4.0 18.6 - - - +
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Residues in contact with GLN 404 (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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402R ASN* 4.1 11.9 + - - +
403R SER* 1.3 72.8 - - - +
405R LYS* 1.3 70.8 + - - +
406R VAL* 3.6 3.3 + - + +
418R TYR* 3.9 2.5 - - - -
419R ASN* 3.1 39.6 + - + +
421R GLN* 4.2 18.7 + - - +
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Residues in contact with LYS 405 (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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403R SER 4.1 0.2 + - - -
404R GLN* 1.3 79.7 + - - +
406R VAL* 1.3 63.6 + - - +
407R SER* 3.6 15.8 + - - +
410R SER* 3.6 19.9 + - - +
416R ASP* 4.2 23.5 + - - -
417R GLN 3.8 1.3 - - - +
418R TYR* 3.5 42.8 + - + -
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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