Contacts of the strand formed by residues 407 - 410 (chain C) in PDB entry 1G88
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 407 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387C VAL* 3.9 32.3 - - + -
399C VAL* 5.0 1.1 - - + -
401C CYS* 4.1 9.6 - - + -
403C SER* 5.0 3.1 - - - -
405C HIS 4.2 3.1 - - - +
406C ALA* 1.3 77.2 - - - +
408C PHE* 1.3 63.6 + - - +
409C VAL* 4.7 1.1 - - + -
427C HIS 3.6 0.3 - - - +
428C LYS* 3.2 3.5 - - - -
429C ILE* 2.6 58.2 + - + +
503C MET* 4.1 17.5 - - + -
504C SER 3.5 9.6 - - - +
505C PHE* 3.9 25.4 - - + -
506C VAL 4.7 0.9 - - - +
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Residues in contact with PHE 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 4.1 3.6 - - + -
406C ALA* 3.9 17.7 - - + -
407C VAL* 1.3 78.3 - - - +
409C VAL* 1.3 61.4 + - - +
426C VAL* 3.6 27.1 - - + -
427C HIS 3.2 4.5 - - - -
428C LYS* 3.8 34.1 - - + -
503C MET* 3.4 0.6 - - - -
504C SER 3.0 23.8 + - - +
506C VAL 4.0 7.6 - - - -
507C LYS 3.8 7.2 - - - -
508C GLY* 3.4 36.3 - - - -
509C TRP* 3.0 29.6 - - + -
513C TYR* 3.2 30.3 - + - -
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Residues in contact with VAL 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C VAL* 4.8 8.1 - - + -
407C VAL* 4.0 1.3 - - + -
408C PHE* 1.3 75.1 - - - +
410C GLN* 1.3 75.2 + - - +
411C SER* 3.8 15.3 - - - -
414C LEU* 4.5 2.0 - - + -
426C VAL* 3.9 3.6 - - - -
427C HIS* 2.6 43.4 + - + +
429C ILE* 4.1 20.6 - - + -
437C VAL* 4.5 12.6 - - + -
501C LEU* 5.0 6.3 - - + -
502C ARG 3.2 7.6 - - - +
503C MET* 3.5 36.6 - - + -
509C TRP* 4.3 1.6 - - - -
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Residues in contact with GLN 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C VAL* 1.3 74.6 - - - +
411C SER* 1.3 60.3 + - - +
412C TYR* 3.9 28.3 + - - -
415C ASP* 5.7 1.8 - - - +
423C GLY* 5.3 11.1 + - - +
425C ALA 4.7 10.3 - - - +
427C HIS* 4.6 1.6 - - - -
497C ARG 5.3 0.2 - - - +
500C ILE 4.3 7.3 - - - +
501C LEU* 3.8 6.6 - - - -
502C ARG* 2.6 68.1 + - + +
509C TRP* 4.1 20.5 - - + -
518C ILE* 5.9 0.8 - - - +
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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