Contacts of the strand formed by residues 306 - 312 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A HIS* 4.0 4.0 - - - -
37A GLY* 3.6 11.4 - - - -
39A VAL* 3.6 29.6 - - + -
297A GLU* 6.6 0.2 - - - -
298A ILE* 4.2 14.6 - - + +
301A LEU* 4.0 25.1 - - + -
302A ASP 3.2 20.9 - - - +
303A ARG* 3.5 11.4 + - - +
304A GLU 3.6 0.8 - - - -
305A GLU* 1.3 81.8 - - - +
307A LEU* 1.3 64.8 + - - +
308A CYS* 3.5 9.9 + - - -
370A ASN* 3.2 20.3 + - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A HIS* 3.5 41.2 - - + +
37A GLY 2.9 12.5 + - - +
38A LEU* 3.3 17.8 - - + +
39A VAL* 3.0 26.9 + - - +
57A LEU* 4.1 34.5 - - + -
62A LYS* 4.5 14.1 - - + +
66A LEU* 5.4 2.9 - - + -
306A VAL* 1.3 70.7 - - - +
308A CYS* 1.3 60.6 + - - +
370A ASN* 3.9 16.4 - - - +
372A ILE* 4.7 9.4 - - + -
405A LEU* 4.5 4.3 - - + -
406A LEU* 4.4 9.2 - - + -
409A HIS* 4.2 12.3 - - + -
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Residues in contact with CYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.6 23.6 - - - -
295A MET* 3.5 26.0 - - - -
296A PRO 5.4 0.7 - - - -
303A ARG* 6.1 2.2 - - - -
306A VAL* 3.5 14.3 + - - -
307A LEU* 1.3 74.2 - - - +
309A VAL* 1.3 56.9 + - - +
310A LYS 4.3 0.2 - - - -
370A ASN* 3.0 12.9 + - - +
371A MET* 3.4 22.1 - - + +
372A ILE* 2.6 35.5 + - - +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.1 12.3 - - + -
39A VAL 3.0 6.5 + - - -
40A LEU* 3.6 22.4 - - + -
41A SER* 3.0 30.1 + - - -
50A TYR* 3.8 20.2 - - + -
53A MET* 4.1 8.7 - - + -
295A MET* 3.3 4.0 - - - +
308A CYS* 1.3 79.4 - - - +
310A LYS* 1.3 63.6 + - - +
372A ILE* 3.3 29.2 - - + +
374A ILE* 3.7 31.2 - - + -
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER* 3.3 15.2 - - - +
293A ASP* 2.7 36.4 + - + +
295A MET* 4.9 7.2 - - + -
308A CYS 4.3 0.4 - - - -
309A VAL* 1.3 76.6 - - - +
311A ALA* 1.3 67.7 + - - +
312A GLU* 3.6 35.5 + - + +
371A MET* 4.9 9.4 - - - -
372A ILE 2.7 11.5 + - - +
373A TYR* 3.3 24.3 - - + -
374A ILE 2.9 23.1 + - - -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER* 3.3 11.4 + - - +
43A GLY* 5.5 7.0 - - - -
44A GLY 5.7 1.0 + - - -
45A ALA* 3.6 31.8 + - + -
49A SER* 5.3 2.5 - - - -
50A TYR* 4.7 7.8 + - + +
293A ASP* 4.9 2.1 - - - +
309A VAL* 4.3 1.0 - - - +
310A LYS* 1.3 80.0 + - - +
312A GLU* 1.3 63.6 + - - +
374A ILE* 3.4 21.3 - - + +
376A THR* 4.1 11.6 - - + +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LYS* 3.6 32.9 + - + +
311A ALA* 1.3 73.7 - - - +
313A ALA* 1.3 71.2 + - - +
316A ALA* 4.2 18.4 - - + +
317A PHE* 3.8 12.5 - - + +
320A ARG* 2.5 36.5 + - - +
373A TYR* 3.3 28.2 - - + -
374A ILE 3.0 9.1 + - - +
375A ASN* 4.1 1.0 - - - -
376A THR* 3.2 26.8 + - - +
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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