Contacts of the strand formed by residues 247 - 251 (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 GLU 247 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241E THR* 3.7 2.9 - - - +
242E ASN* 2.9 29.3 + - - +
245E LYS* 3.6 49.3 + - + +
246E HIS* 1.3 79.3 - - - +
248E LEU* 1.3 71.4 + - - +
292G LEU* 4.1 9.7 - - - +
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Residues in contact with LEU 248 (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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239E VAL* 4.0 13.5 - - + -
240E VAL 3.5 9.0 - - - +
241E THR* 3.8 17.5 - - - +
247E GLU* 1.3 86.0 - - - +
249E GLU* 1.3 62.4 + - - +
250E ARG* 4.1 0.9 + - - +
289E GLY 4.9 4.7 - - - +
294E ASN* 3.4 43.5 - - + +
292G LEU* 3.7 33.2 - - + -
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Residues in contact with GLU 249 (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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239E VAL* 3.4 6.0 - - - +
240E VAL* 3.0 45.2 + - + +
242E ASN* 3.3 31.3 + - + +
245E LYS* 3.6 28.4 + - - +
247E GLU 3.7 3.0 + - - -
248E LEU* 1.3 73.4 - - - +
250E ARG* 1.3 62.2 + - - +
251E TYR* 2.5 34.6 + - + -
280E ASN* 4.6 3.2 + - - -
282E LYS* 5.7 2.6 + - - -
284E GLU* 4.1 5.0 - - - +
286E ILE* 4.0 4.3 - - - +
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Residues in contact with ARG 250 (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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237E SER* 4.3 12.1 + - - -
238E VAL 3.7 2.7 - - - +
239E VAL* 3.9 22.4 - - + -
248E LEU 4.1 1.5 + - - +
249E GLU* 1.3 77.3 - - - +
251E TYR* 1.3 70.0 + - - +
252E SER* 2.7 35.0 + - - +
255E THR* 3.9 23.7 + - - +
256E THR* 4.0 11.4 - - - +
297E GLU 5.0 7.4 + - - +
298E ILE* 5.7 0.6 - - - +
299E GLU* 2.6 47.4 + - - +
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Residues in contact with TYR 251 (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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215E LEU* 4.6 7.4 - - + +
236E LEU 4.1 0.5 - - - +
237E SER* 3.2 1.7 - - - -
238E VAL* 2.9 41.3 + - - +
240E VAL* 3.5 32.5 - - + -
249E GLU* 2.5 30.2 + - + -
250E ARG* 1.3 75.6 - - - +
252E SER* 1.3 61.8 + - - +
256E THR* 3.3 32.1 - - + +
259E GLN* 3.7 30.8 + - + -
264E VAL* 3.5 29.4 - - + -
267E TRP* 3.7 13.0 - + - -
280E ASN* 4.3 6.8 + - - +
286E ILE* 3.6 13.5 - - - +
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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