Contacts of the strand formed by residues 425 - 429 (chain R) 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 LEU 425 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415R ILE* 4.0 21.1 - - + -
416R SER 3.3 11.7 - - - +
417R GLY* 4.3 0.9 - - - -
423R ASN 4.7 0.2 - - - +
424R GLN* 1.3 79.9 - - - +
426R VAL* 1.3 64.5 + - - +
437R ALA 3.9 0.2 - - - +
438R GLU* 3.3 4.0 - - - -
439R LEU* 2.7 52.3 + - + +
442R HIS* 4.2 5.8 - - + -
446R VAL* 4.1 15.9 - - + -
449R LEU* 4.0 18.8 - - + -
458R VAL 4.5 2.0 - - - +
460R SER* 3.8 29.6 - - - +
470R TRP* 3.6 30.7 - - + +
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Residues in contact with VAL 426 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398R ALA 5.9 0.9 - - - +
415R ILE* 3.3 4.7 - - - -
416R SER* 3.0 32.0 + - - +
418R HIS* 4.0 11.0 - - - +
424R GLN* 3.8 25.1 - - + +
425R LEU* 1.3 79.2 - - - +
427R ILE* 1.3 68.6 + - - +
428R TRP* 3.5 39.1 - - + +
435R LYS* 3.8 28.7 - - + +
437R ALA 3.4 8.5 - - - +
438R GLU* 3.9 12.6 - - + +
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Residues in contact with ILE 427 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168R ILE* 4.0 23.8 - - + -
413R GLU* 3.2 39.3 - - + +
414R LEU 3.2 7.6 - - - +
415R ILE* 3.8 32.1 - - + -
426R VAL* 1.3 73.4 - - - +
428R TRP* 1.3 59.7 + - - +
435R LYS* 3.5 4.2 - - - -
436R VAL* 2.7 37.7 + - + -
437R ALA* 2.7 36.4 + - + +
439R LEU* 4.3 12.3 - - + -
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Residues in contact with TRP 428 (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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382R ILE* 3.5 24.8 - - + +
396R VAL* 4.1 22.0 - - + -
397R ASP 4.1 17.7 - - - -
398R ALA* 4.6 9.2 - - + -
413R GLU* 3.3 8.8 - - - +
414R LEU* 2.8 54.8 + - + +
416R SER* 2.9 24.5 + - - -
418R HIS* 4.9 0.2 - - - -
426R VAL* 3.5 34.4 + - + +
427R ILE* 1.3 72.6 - - - +
429R LYS* 1.3 60.1 + - - +
430R TYR 3.8 0.2 + - - -
433R MET* 3.6 44.6 - - + -
434R ALA 3.7 4.7 - - - +
435R LYS* 3.6 37.7 - - + -
436R VAL* 4.4 0.9 - - - -
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Residues in contact with LYS 429 (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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411R TYR 2.9 15.2 + - - +
412R LYS* 2.9 31.0 + - - +
413R GLU* 3.8 16.8 - - + +
414R LEU* 5.0 0.2 - - - -
428R TRP* 1.3 70.6 - - - +
430R TYR* 1.3 72.8 + - - +
431R PRO 3.8 0.2 - - - -
432R THR* 3.3 23.1 + - + +
433R MET* 2.7 38.0 + - - +
434R ALA* 2.9 17.1 + - + +
436R VAL* 3.7 13.2 - - + +
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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