Contacts of the strand formed by residues 401 - 410 (chain Y) in PDB entry 2CKV
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 GLU 401 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311Y ILE* 4.3 8.1 - - - +
312Y SER* 4.0 16.0 + - - -
383Y SER* 2.9 27.3 + - - +
384Y GLY 5.7 0.2 - - - +
395Y TYR* 2.8 25.6 + - - -
397Y VAL* 3.5 12.8 - - + +
398Y ARG* 2.7 48.4 + - + +
399Y ASN 3.4 3.4 + - - +
400Y GLY* 1.3 80.5 - - - +
402Y ASN* 1.3 59.9 + - - +
403Y LEU* 3.9 7.0 + - + +
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Residues in contact with ASN 402 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312Y SER* 2.5 36.7 + - - +
313Y VAL 4.0 0.2 - - - -
314Y ASN* 3.7 29.6 + - - +
324Y PHE* 5.7 2.2 - - - -
383Y SER* 3.4 1.2 - - - -
384Y GLY* 2.9 39.1 + - - +
400Y GLY 3.9 1.9 + - - +
401Y GLU* 1.3 73.5 - - - +
403Y LEU* 1.3 64.7 + - - +
404Y GLU* 3.9 5.2 + - - +
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Residues in contact with LEU 403 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311Y ILE* 5.3 5.6 - - + +
312Y SER 3.5 4.2 + - - +
313Y VAL* 3.4 9.1 - - + +
314Y ASN 3.0 23.2 + - - -
335Y PHE* 3.4 53.4 - - + -
381Y LEU* 4.0 7.6 - - + -
382Y LEU 3.4 11.2 - - - +
383Y SER* 3.8 19.7 - - - -
388Y LEU* 3.9 29.2 - - + -
395Y TYR* 3.9 18.6 - - + -
397Y VAL* 4.7 3.1 - - + -
401Y GLU* 3.9 16.1 + - + +
402Y ASN* 1.3 74.9 + - - +
404Y GLU* 1.3 59.4 + - - +
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Residues in contact with GLU 404 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314Y ASN* 3.3 31.3 + - + +
316Y SER* 2.8 31.4 + - - +
380Y GLU 3.6 0.3 - - - +
381Y LEU* 3.7 4.7 - - - +
382Y LEU* 2.6 45.9 + - + +
383Y SER 5.0 4.5 - - - +
384Y GLY* 6.1 1.0 - - - -
385Y GLY 5.8 1.0 + - - -
402Y ASN* 3.9 6.8 + - - +
403Y LEU* 1.3 74.7 - - - +
405Y VAL* 1.3 66.2 + - - +
406Y ARG* 2.9 44.4 + - + -
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Residues in contact with VAL 405 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313Y VAL* 4.9 7.9 - - + -
314Y ASN 2.9 17.6 + - - +
315Y TYR* 3.8 19.5 - - + -
316Y SER 3.6 18.9 + - - +
335Y PHE* 4.9 4.3 - - + -
339Y MET* 4.3 15.0 - - + -
350Y PHE* 6.5 1.1 - - + -
363Y ILE* 6.0 2.9 - - + -
366Y ILE* 3.7 30.5 - - + -
379Y TRP* 4.8 5.2 - - + +
380Y GLU 3.3 6.3 - - - +
381Y LEU* 3.5 30.7 - - + -
404Y GLU* 1.3 71.5 - - - +
406Y ARG* 1.3 63.2 + - - +
407Y TRP 4.1 1.0 + - - -
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Residues in contact with ARG 406 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316Y SER* 3.5 18.4 + - - +
317Y VAL* 4.6 7.8 - - + +
378Y TYR 3.3 1.2 - - - +
379Y TRP* 3.3 7.1 - - - -
380Y GLU* 2.7 47.7 + - + +
382Y LEU* 3.8 38.4 - - + +
383Y SER 5.7 0.4 + - - -
385Y GLY* 5.7 4.2 + - - +
404Y GLU* 2.9 39.2 + - - +
405Y VAL* 1.3 72.1 - - - +
407Y TRP* 1.3 59.7 + - - +
408Y SER* 3.4 9.0 + - - +
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Residues in contact with TRP 407 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315Y TYR* 5.0 2.2 - - - +
316Y SER 4.3 1.3 + - - +
317Y VAL* 3.5 49.3 - - + +
318Y ARG* 5.3 9.0 - - + -
369Y LEU* 5.1 19.1 - - + -
370Y CYS 4.0 6.7 - - - -
371Y ALA* 3.8 12.7 + - - +
372Y ASN* 3.6 33.0 - - - -
377Y THR* 3.7 27.2 - - + +
378Y TYR 3.6 15.0 - - - -
379Y TRP* 3.4 40.2 - + + -
405Y VAL 4.1 0.8 + - - -
406Y ARG* 1.3 68.9 - - - +
408Y SER* 1.3 60.5 + - - +
409Y LYS 4.1 0.7 + - - -
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Residues in contact with SER 408 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377Y THR* 4.7 2.7 - - - -
378Y TYR* 3.1 51.8 + - - -
380Y GLU* 4.4 15.6 + - - -
406Y ARG* 3.4 11.4 + - - -
407Y TRP* 1.3 74.6 - - - +
409Y LYS* 1.3 70.4 + - - +
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Residues in contact with LYS 409 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376Y ARG 3.8 17.7 - - - +
377Y THR* 3.9 12.3 - - + +
378Y TYR* 5.3 0.2 - - - -
407Y TRP 4.1 1.2 + - - -
408Y SER* 1.3 82.4 + - - +
410Y TYR* 1.3 71.0 + - - +
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Residues in contact with TYR 410 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Y THR* 6.2 0.2 - - - +
119Y THR 4.4 1.6 + - - -
120Y ASN* 3.8 20.2 - - - -
373Y ASN* 5.4 3.6 + - - -
375Y ASP 5.1 0.2 + - - -
376Y ARG* 3.5 72.5 + - + +
377Y THR 3.9 4.0 - - - -
378Y TYR* 3.5 41.1 - + + -
408Y SER 4.4 0.4 - - - -
409Y LYS* 1.3 85.6 - - - +
1411Y B12 3.1 43.5 + - + +
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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