Contacts of the strand formed by residues 371 - 379 (chain C) in PDB entry 3SV1
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 ILE 371 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B ARG 3.8 3.1 - - - -
410B LYS* 3.2 42.0 - - + +
411B ALA* 3.9 12.1 - - + +
414B ILE* 4.1 20.2 - - + -
366C ASP* 4.4 7.9 - - + +
367C LEU* 4.2 27.8 - - + -
370C GLY* 1.3 79.1 - - - +
372C ILE* 1.3 63.0 + - - +
373C PHE* 3.9 27.5 + - + -
432C LEU 3.4 1.7 - - - +
433C PHE* 3.7 0.2 - - - -
434C ILE* 3.0 31.2 + - + +
516C SER* 4.4 8.1 - - - -
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Residues in contact with ILE 372 (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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404B ARG* 3.4 41.1 - - - +
407B ARG* 3.4 34.8 + - + +
408B MET* 3.5 25.1 - - + +
411B ALA* 3.8 7.7 - - - +
371C ILE* 1.3 76.4 - - - +
373C PHE* 1.3 59.6 + - - +
374C ALA* 5.4 0.5 - - - +
431C ASP* 3.2 38.7 - - + +
432C LEU 3.2 13.9 - - - +
433C PHE* 3.7 19.5 - - + +
442C LEU* 4.5 5.8 - - + -
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Residues in contact with PHE 373 (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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411B ALA* 4.1 29.6 - - + -
414B ILE* 5.0 9.9 - - + -
415B LYS* 5.3 7.0 - - + -
371C ILE* 3.9 23.8 - - + -
372C ILE* 1.3 75.6 - - - +
374C ALA* 1.3 57.0 + - - +
431C ASP* 3.4 2.9 - - - -
432C LEU* 2.5 46.8 + - + -
434C ILE* 3.9 17.5 - - + -
509C ASP* 4.6 15.3 - - + +
512C LEU* 4.3 23.1 - - + -
513C ILE* 3.9 30.7 - - + -
516C SER* 3.4 26.7 - - - -
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Residues in contact with ALA 374 (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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404B ARG* 5.5 1.6 - - - +
373C PHE* 1.3 77.9 - - - +
375C ALA* 1.3 62.9 + - - +
430C VAL 3.2 14.4 - - - +
431C ASP* 3.6 15.0 - - - +
444C ALA* 5.5 2.5 - - + -
507C SER* 3.6 9.9 + - - -
509C ASP* 4.3 4.1 + - - +
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Residues in contact with ALA 375 (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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373C PHE 4.3 0.4 + - - -
374C ALA* 1.3 73.3 - - - +
376C ASN* 1.3 70.5 + - - +
429C GLU* 4.0 0.7 - - - +
430C VAL* 3.0 32.4 + - - +
432C LEU* 4.4 14.5 - - + +
505C PHE* 4.6 5.6 - - + -
506C GLU 3.1 15.7 - - - +
507C SER* 3.2 22.7 - - - +
513C ILE* 4.3 7.2 - - + -
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Residues in contact with ASN 376 (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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375C ALA* 1.3 80.0 + - - +
377C TYR* 1.3 61.9 + - - +
378C LEU* 3.8 2.0 + - + +
427C LEU* 3.1 36.6 - - + +
428C THR 3.9 0.2 - - - -
429C GLU* 4.0 18.4 + - - +
505C PHE* 2.9 33.0 - - - -
506C GLU* 2.8 45.7 + - + +
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Residues in contact with TYR 377 (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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376C ASN* 1.3 73.5 - - - +
378C LEU* 1.3 58.8 + - - +
379C GLY* 3.3 27.0 - - - -
380C SER* 2.7 35.1 + - - -
426C THR 4.6 0.3 - - - +
427C LEU* 3.6 2.7 - - - -
428C THR* 3.0 47.3 + - + +
430C VAL* 4.0 9.2 - - + -
450C MET* 3.3 27.4 - - + -
451C MET* 3.7 18.9 - - + +
503C HIS* 4.2 3.6 - - + -
504C VAL 3.3 10.5 - - - -
505C PHE* 3.2 34.5 - + + -
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Residues in contact with LEU 378 (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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376C ASN 4.7 1.1 - - - +
377C TYR* 1.3 73.0 - - - +
379C GLY* 1.3 57.5 + - - +
405C VAL* 3.8 14.3 - - + +
406C LYS* 5.1 13.5 - - + -
408C MET* 3.5 5.9 - - - +
409C GLN* 2.6 48.0 + - + +
426C THR 4.6 0.9 - - - +
427C LEU* 4.3 16.8 - - + -
467C ILE* 5.7 2.5 - - + -
504C VAL* 3.4 20.9 + - + -
505C PHE* 3.4 34.1 - - - +
506C GLU* 3.8 18.2 - - + +
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Residues in contact with GLY 379 (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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377C TYR* 3.3 27.6 - - - -
378C LEU* 1.3 80.7 - - - +
380C SER* 1.3 59.7 + - - -
405C VAL* 3.4 7.9 - - - +
408C MET* 4.6 6.1 - - - -
504C VAL* 3.0 31.5 + - - +
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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