Contacts of the strand formed by residues 306 - 312 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E GLY* 3.8 11.7 - - - -
39E VAL* 3.6 29.8 - - + -
297E GLU* 6.4 0.2 - - - -
298E ILE* 4.3 15.5 - - + +
301E LEU* 3.7 30.7 - - + -
302E ASP 3.2 19.3 - - - +
303E ARG* 3.4 9.8 + - - +
304E GLU 3.3 2.6 - - - -
305E GLU* 1.3 83.1 - - - +
307E LEU* 1.3 62.8 + - - +
308E CYS* 3.6 10.4 + - - -
370E ASN* 3.3 20.6 - - - +
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Residues in contact with LEU 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E HIS* 3.8 25.6 - - + +
37E GLY 3.1 13.6 + - - +
38E LEU* 3.4 18.1 - - + +
39E VAL* 3.0 27.0 + - - +
57E LEU* 4.0 27.8 - - + -
62E LYS* 4.5 13.5 - - + +
66E LEU* 5.8 3.8 - - + -
305E GLU 4.2 0.8 - - - -
306E VAL* 1.3 71.9 - - - +
308E CYS* 1.3 58.6 + - - +
370E ASN* 3.5 30.1 - - - +
372E ILE* 4.6 7.6 - - + -
405E LEU* 4.2 17.3 - - + -
406E LEU* 4.6 7.2 - - + -
409E HIS* 4.2 5.8 - - + -
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Residues in contact with CYS 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E VAL* 3.6 24.5 - - - -
295E MET* 3.5 26.7 - - - -
296E PRO 5.5 0.2 - - - -
303E ARG* 5.8 3.1 - - - -
306E VAL* 3.9 14.4 - - - -
307E LEU* 1.3 75.0 - - - +
309E VAL* 1.3 57.6 + - - +
370E ASN* 2.8 15.6 + - - +
371E MET* 3.4 20.1 - - + +
372E ILE* 2.6 36.6 + - - +
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Residues in contact with VAL 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LEU* 4.2 11.2 - - + -
39E VAL 3.1 7.1 + - - -
40E LEU* 3.7 21.8 - - + -
41E SER* 3.0 29.8 + - - -
50E TYR* 4.0 19.1 - - + -
53E MET* 4.0 11.7 - - + -
295E MET* 3.7 3.2 - - - +
308E CYS* 1.3 78.9 - - - +
310E LYS* 1.3 62.3 + - - +
311E ALA 5.0 0.2 - - - +
372E ILE* 3.4 29.6 - - + +
374E ILE* 3.6 31.0 - - + -
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Residues in contact with LYS 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E SER* 3.5 15.5 - - - +
293E ASP* 2.9 31.0 + - + +
295E MET* 4.7 5.8 - - + -
308E CYS 4.2 0.4 - - - -
309E VAL* 1.3 74.1 - - - +
311E ALA* 1.3 65.6 + - - +
312E GLU* 3.5 37.8 + - + +
371E MET* 4.6 14.6 - - - -
372E ILE 2.8 11.4 + - - +
373E TYR* 3.4 22.9 - - + -
374E ILE 3.1 20.6 + - - -
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Residues in contact with ALA 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E SER* 3.4 9.8 + - - +
43E GLY* 5.7 3.6 - - - -
44E GLY 5.6 2.4 + - - -
45E ALA* 3.6 33.1 + - + +
49E SER* 4.9 6.5 - - - -
50E TYR* 4.5 11.4 + - + +
309E VAL* 4.2 1.8 - - - +
310E LYS* 1.3 75.5 + - - +
312E GLU* 1.3 62.5 + - - +
374E ILE* 3.5 17.3 - - + +
376E THR* 3.8 12.7 - - + +
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Residues in contact with GLU 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E LYS* 3.5 33.4 + - + +
311E ALA* 1.3 73.9 - - - +
313E ALA* 1.3 69.7 + - - +
316E ALA* 4.3 13.5 - - + +
317E PHE* 3.4 19.4 - - + +
320E ARG* 2.6 34.2 + - - +
373E TYR* 3.4 27.7 - - + -
374E ILE 2.9 10.5 + - - +
375E ASN* 3.9 0.5 - - - -
376E THR* 2.8 31.7 + - - +
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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