Contacts of the strand formed by residues 507 - 512 (chain C) in PDB entry 3SRF
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 507 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422C CYS* 3.8 35.2 - - + +
423C LEU 5.6 0.2 - - - +
424C ALA* 3.5 4.5 - - + -
425C ALA* 2.9 28.4 + - - +
505C GLY 5.0 3.4 - - - +
506C ASP* 1.3 78.0 + - - +
508C VAL* 1.3 68.9 + - - +
526C VAL* 3.6 27.6 - - + -
527C VAL 4.0 3.6 - - - +
528C PRO* 5.6 3.1 - - + -
407G LEU* 4.0 26.7 - - + -
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Residues in contact with VAL 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ALA* 4.3 0.7 - - - -
425C ALA* 4.6 0.7 - - + -
426C ALA* 3.5 30.7 - - + +
428C ILE* 4.1 7.9 - - + -
493C MET* 3.8 25.8 - - + -
502C PHE* 4.3 8.5 - - + -
507C VAL* 1.3 79.6 - - - +
509C ILE* 1.3 64.9 + - - +
510C VAL* 4.0 9.4 + - + -
526C VAL* 3.6 5.7 - - - +
527C VAL* 3.3 46.9 + - + +
528C PRO 5.1 0.2 - - - +
529C VAL* 4.1 19.1 - - + -
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Residues in contact with ILE 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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415C SER* 4.0 30.1 - - - +
418C ALA* 3.8 16.4 - - + -
419C SER* 4.1 8.3 - - - +
422C CYS* 4.1 18.8 - - - -
424C ALA* 4.1 12.1 - - + -
426C ALA 3.1 5.7 + - - +
427C LEU* 3.3 12.0 - - + +
428C ILE* 2.7 32.2 + - - +
508C VAL* 1.3 76.6 - - - +
510C VAL* 1.3 59.9 + - - +
511C LEU* 4.1 3.2 + - + +
524C MET* 3.6 28.7 - - + -
525C ARG 3.3 2.2 - - - +
526C VAL* 3.7 24.9 - - + -
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Residues in contact with VAL 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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428C ILE* 3.4 20.0 - - + +
430C LEU* 5.3 0.2 - - + -
489C VAL* 3.7 25.8 - - + -
493C MET* 5.6 0.4 - - - -
508C VAL* 4.0 10.8 - - + -
509C ILE* 1.3 76.7 - - - +
511C LEU* 1.3 63.8 + - - +
512C THR* 3.7 24.0 + - + -
523C THR 3.5 1.6 - - - +
524C MET* 3.5 2.6 - - - -
525C ARG* 2.8 57.1 + - + +
527C VAL* 3.6 27.8 - - + -
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Residues in contact with LEU 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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408C MET* 5.0 1.3 - - + -
411C MET* 3.6 32.3 - - + +
412C ALA* 5.7 0.2 - - - -
415C SER* 3.3 37.7 - - - +
427C LEU* 4.4 10.8 - - + -
428C ILE 2.7 13.1 + - - +
429C VAL* 3.5 23.2 - - + -
430C LEU 3.0 24.3 + - - -
440C VAL* 4.0 15.7 - - + -
509C ILE* 4.8 3.6 - - + -
510C VAL* 1.3 72.3 - - - +
512C THR* 1.3 61.2 + - - +
521C THR* 2.8 34.3 + - + +
523C THR 3.3 5.2 - - - +
524C MET* 4.3 2.2 - - + -
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Residues in contact with THR 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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430C LEU* 4.0 19.3 - - + -
485C VAL* 3.8 22.3 - - + +
489C VAL* 4.0 1.8 - - + -
510C VAL* 3.7 16.0 + - + -
511C LEU* 1.3 78.6 - - - +
513C GLY* 1.3 68.0 + - - +
514C TRP* 5.3 0.3 - - - -
521C THR* 3.2 10.4 + - - -
522C ASN 3.4 0.5 + - - -
523C THR* 2.9 42.3 + - - +
525C ARG* 3.5 29.4 + - - +
514G TRP* 5.5 1.6 - - - -
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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