Contacts of the strand formed by residues 235 - 242 (chain G) 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 ASN 235 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G THR 2.8 14.3 + - - +
68G HIS* 3.3 41.9 + - + +
69G VAL 3.1 20.0 + - - +
222G ARG* 3.7 9.6 - - - +
234G LYS* 1.3 68.4 - - - +
236G LEU* 1.3 65.8 + - - +
237G SER* 3.7 3.8 + - - -
252G SER* 5.0 0.9 - - - -
253G GLU* 3.3 35.5 + - - +
254G ASP* 3.6 27.3 + - - +
601G EDO 5.8 1.5 - - - -
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Residues in contact with LEU 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G VAL 3.4 9.6 - - - +
79G ALA* 3.8 32.1 - - + +
80G SER* 4.0 14.1 - - - +
83G ALA* 3.7 13.7 - - + -
215G LEU* 3.7 17.2 - - + +
218G LEU* 3.7 15.0 - - + +
234G LYS 2.9 5.8 + - - -
235G ASN* 1.3 73.6 + - - +
237G SER* 1.3 70.0 + - - +
238G VAL* 4.0 23.6 - - + -
252G SER* 3.6 1.2 - - - -
253G GLU* 3.4 27.1 + - - +
261G ILE* 3.7 30.3 - - + -
265G VAL* 5.1 1.1 - - + -
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Residues in contact with SER 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G HIS* 5.8 0.2 - - - +
69G VAL 3.1 8.3 + - - +
70G SER* 3.1 24.7 + - - -
71G GLY 3.0 22.9 + - - -
215G LEU* 5.4 0.2 - - - -
235G ASN* 4.2 3.5 + - - -
236G LEU* 1.3 77.0 - - - +
238G VAL* 1.3 64.1 + - - +
239G VAL* 5.4 0.4 - - - -
250G ARG* 5.2 0.4 - - - -
251G TYR 3.4 5.2 - - - -
252G SER* 3.2 13.7 - - - -
298G ILE* 5.0 0.5 - - - +
601G EDO 3.1 37.1 + - - -
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Residues in contact with VAL 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G GLY 3.2 12.3 - - - +
76G ALA* 3.9 33.4 - - + +
79G ALA* 5.4 0.2 - - + -
215G LEU* 5.7 4.7 - - + -
236G LEU* 4.0 19.5 - - + -
237G SER* 1.3 79.2 - - - +
239G VAL* 1.3 63.6 + - - +
240G VAL* 4.2 0.6 + - - -
249G GLU 4.4 0.2 - - - +
250G ARG* 3.9 1.8 - - - +
251G TYR* 3.1 36.0 + - + +
264G VAL* 3.5 39.3 - - + +
265G VAL* 4.4 8.5 - - + +
268G SER* 4.8 2.2 - - - -
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Residues in contact with VAL 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G SER* 4.6 4.9 - - - +
71G GLY 3.1 9.6 + - - +
72G ALA* 3.7 11.4 - - + +
237G SER 5.4 0.2 - - - -
238G VAL* 1.3 79.4 - - - +
240G VAL* 1.3 69.6 + - - +
248G LEU* 3.9 26.2 - - + -
249G GLU 3.8 11.7 - - - +
250G ARG* 4.7 16.2 - - + +
268G SER* 2.8 27.4 + - - -
289G GLY* 3.7 9.7 - - - +
294G ASN* 4.6 5.6 - - - +
296G PRO* 3.9 30.3 - - + -
601G EDO 5.6 0.9 - - - +
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Residues in contact with VAL 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239G VAL* 1.3 79.4 - - - +
241G THR* 1.3 64.4 + - - +
242G ASN* 5.6 0.2 - - - -
248G LEU* 3.4 11.1 - - - +
249G GLU* 2.9 45.5 + - + +
251G TYR* 3.7 20.0 - - + -
264G VAL* 3.8 20.2 - - + +
267G TRP* 3.9 7.9 - - + -
268G SER* 3.6 28.5 - - - +
286G ILE* 3.7 17.5 - - + -
287G ALA 3.8 7.0 - - - +
289G GLY* 3.7 8.1 - - - +
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Residues in contact with THR 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E ILE* 4.3 10.8 - - + -
292E LEU* 3.6 26.4 - - + +
240G VAL* 1.3 77.0 - - - +
242G ASN* 1.3 68.7 + - - +
243G GLN* 3.5 16.3 + - + +
247G GLU 4.0 2.2 - - - -
248G LEU* 3.3 17.1 - - - +
286G ILE* 3.6 4.5 - - - +
287G ALA 3.1 28.4 + - - -
288G ASP 2.8 24.0 + - - -
289G GLY* 3.4 5.9 - - - -
291G ILE* 4.5 10.6 + - + +
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Residues in contact with ASN 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240G VAL* 4.1 0.8 + - + -
241G THR* 1.3 71.5 - - - +
243G GLN* 1.3 54.9 + - - +
244G THR* 3.1 10.5 + - - -
245G LYS* 2.7 40.1 + - - +
246G HIS* 2.7 36.7 + - - -
247G GLU* 2.9 27.2 + - + +
249G GLU* 3.2 26.9 + - + +
284G GLU* 3.2 33.6 + - - +
285G TYR 3.9 1.1 + - - -
286G ILE* 3.9 12.9 - - - +
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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