Contacts of the strand formed by residues 508 - 513 (chain C) in PDB entry 4QGC
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 508 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423C CYS* 4.4 23.7 + - + +
424C CYS 5.8 0.6 + - - -
425C SER* 3.2 26.7 - - - +
426C GLY 3.4 5.2 + - - -
506C GLY 4.4 5.8 - - - +
507C ASP* 1.3 82.7 - - - +
509C VAL* 1.3 67.6 + - - +
527C VAL* 3.6 31.0 - - + -
528C VAL 3.7 10.1 - - - +
529C PRO* 4.5 8.7 - - + -
406D SER* 4.1 20.2 - - - +
408D PRO* 5.2 5.4 - - + -
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Residues in contact with VAL 509 (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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425C SER* 4.0 0.7 - - - -
426C GLY 4.6 0.7 - - - +
427C ALA* 3.7 16.6 - - + +
429C ILE* 4.2 13.5 - - + -
494C MET* 3.6 28.5 - - + -
503C PHE* 3.8 31.9 - - + -
508C VAL* 1.3 80.4 - - - +
510C ILE* 1.3 67.1 + - - +
511C VAL* 4.3 6.3 - - + -
526C ARG 3.7 0.3 - - - +
527C VAL* 3.8 2.8 - - - -
528C VAL* 2.9 41.9 + - + +
530C VAL* 3.7 18.2 - - + -
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Residues in contact with ILE 510 (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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416C ALA* 4.0 30.3 - - + +
419C ALA* 3.7 22.7 - - + +
420C SER* 4.1 6.3 - - - +
423C CYS* 4.6 2.2 - - - -
425C SER* 3.3 26.5 - - - +
427C ALA 3.2 4.6 + - - +
428C ILE* 3.4 12.0 - - + -
429C ILE* 2.7 33.1 + - - +
509C VAL* 1.3 78.5 - - - +
511C VAL* 1.3 60.9 + - - +
512C LEU* 4.3 2.2 - - + -
525C MET* 3.7 28.3 - - + -
526C ARG 3.6 2.7 - - - +
527C VAL* 4.1 21.5 - - + -
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Residues in contact with VAL 511 (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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429C ILE* 3.3 30.1 - - + +
431C LEU* 5.2 0.4 - - + -
490C VAL* 3.9 27.8 - - + -
509C VAL* 4.3 4.3 - - + -
510C ILE* 1.3 81.1 - - - +
512C LEU* 1.3 64.7 + - - +
513C THR* 3.8 22.7 + - + +
524C THR 3.5 1.0 - - - +
525C MET* 3.4 4.3 - - - -
526C ARG* 2.8 52.6 + - + +
528C VAL* 3.6 24.2 - - + -
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Residues in contact with LEU 512 (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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412C THR* 3.7 25.4 - - + +
413C ALA* 4.5 3.1 - - - -
416C ALA* 3.7 21.8 - - + -
428C ILE* 4.6 4.0 - - + -
429C ILE 2.7 13.3 + - - +
430C VAL* 4.2 15.4 - - + +
431C LEU 3.1 26.3 + - - +
437C SER* 5.1 0.9 - - - +
441C VAL* 3.7 31.0 - - + -
510C ILE* 4.6 0.7 - - + -
511C VAL* 1.3 78.7 - - - +
513C THR* 1.3 65.7 + - - +
522C THR* 4.1 15.9 - - + -
524C THR 3.3 10.8 - - - +
525C MET* 3.7 18.2 - - + -
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Residues in contact with THR 513 (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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431C LEU* 3.7 32.5 - - + -
482C TRP* 4.5 7.2 - - - -
486C VAL* 3.9 15.7 - - + -
511C VAL* 3.8 19.0 + - + +
512C LEU* 1.3 80.8 - - - +
514C GLY* 1.3 71.9 + - - +
522C THR* 3.5 10.0 - - - +
523C ASN 3.5 5.7 + - - -
524C THR* 3.0 41.4 + - - +
526C ARG* 4.6 5.4 + - + +
515D TRP* 5.0 4.2 - - - -
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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