Contacts of the strand formed by residues 306 - 312 (chain C) in PDB entry 4KYI
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 306 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C HIS* 4.2 1.3 - - - -
37C GLY* 3.6 4.9 - - - +
39C VAL* 3.7 28.0 - - + -
297C GLU* 6.3 0.9 - - - -
298C ILE* 4.2 18.6 - - + +
301C LEU* 3.7 30.3 - - + -
302C ASP 3.3 19.7 - - - +
303C ARG* 3.5 9.5 + - - +
304C GLU 3.4 3.0 + - - -
305C GLU* 1.3 82.8 - - - +
307C LEU* 1.3 64.9 + - - +
308C CYS* 3.6 11.5 + - - -
370C ASN* 3.2 20.5 - - - +
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Residues in contact with LEU 307 (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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35C HIS* 3.4 41.7 - - + +
37C GLY 2.9 11.9 + - - +
38C LEU* 3.5 17.6 - - + +
39C VAL* 2.9 28.2 + - - +
57C LEU* 4.1 33.4 - - + -
62C LYS* 4.7 12.1 - - + +
66C LEU* 5.1 6.1 - - + -
306C VAL* 1.3 69.8 - - - +
308C CYS* 1.3 60.9 + - - +
370C ASN* 3.8 15.7 - - + +
372C ILE* 4.7 10.8 - - + -
405C LEU* 4.6 14.4 - - + -
406C LEU* 4.6 4.5 - - + -
409C HIS* 4.6 3.4 - - + -
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Residues in contact with CYS 308 (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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39C VAL* 3.6 21.5 - - - -
295C MET* 3.6 29.2 - - - -
296C PRO 5.3 1.1 - - - -
303C ARG* 6.4 1.8 - - - -
306C VAL* 4.2 14.1 - - - -
307C LEU* 1.3 73.5 - - - +
309C VAL* 1.3 56.7 + - - +
310C LYS 4.1 0.2 - - - -
370C ASN* 2.8 16.2 + - - +
371C MET* 3.4 19.7 - - + +
372C ILE* 2.6 35.0 + - - +
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Residues in contact with VAL 309 (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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38C LEU* 3.9 14.4 - - + -
39C VAL 3.0 7.1 + - - +
40C LEU* 3.7 23.2 - - + -
41C SER* 2.9 30.4 + - - -
50C TYR* 3.9 18.5 + - + -
53C MET* 4.2 9.0 - - + -
295C MET* 4.1 2.1 - - - +
308C CYS* 1.3 76.3 - - - +
310C LYS* 1.3 63.2 + - - +
311C ALA 4.3 0.6 + - - -
372C ILE* 3.3 33.0 - - + +
374C ILE* 3.8 29.4 - - + -
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Residues in contact with LYS 310 (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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41C SER* 3.3 16.8 + - - +
293C ASP* 3.6 34.8 + - - +
294C ASN 5.7 0.2 - - - +
295C MET* 5.0 5.2 - - + -
308C CYS 4.1 0.6 + - - -
309C VAL* 1.3 77.2 - - - +
311C ALA* 1.3 68.5 + - - +
312C GLU* 3.5 30.8 + - + +
371C MET* 4.6 9.9 - - - -
372C ILE 2.8 10.1 + - - -
373C TYR* 3.4 32.9 - - + +
374C ILE 2.8 24.3 + - - -
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Residues in contact with ALA 311 (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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41C SER* 3.5 8.5 + - - +
43C GLY* 5.6 6.3 - - - -
45C ALA* 3.6 22.0 - - + +
49C SER* 5.5 2.2 - - - -
50C TYR* 4.6 10.9 + - + +
293C ASP* 5.3 4.3 - - - +
309C VAL* 4.3 1.0 + - - +
310C LYS* 1.3 81.2 + - - +
312C GLU* 1.3 62.3 + - - +
374C ILE* 3.3 15.7 - - + +
376C THR* 3.6 23.4 - - + +
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Residues in contact with GLU 312 (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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310C LYS* 3.5 36.7 + - + +
311C ALA* 1.3 73.5 - - - +
313C ALA* 1.3 64.9 + - - +
316C ALA* 3.8 15.6 - - + +
317C PHE* 3.8 9.1 - - + +
320C ARG* 2.2 40.5 + - - +
373C TYR* 3.8 20.2 - - + -
374C ILE 3.0 9.6 + - - +
375C ASN* 3.9 1.9 - - - -
376C THR* 2.3 36.1 + - - -
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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