Contacts of the strand formed by residues 235 - 242 (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 ASN 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR 2.8 18.9 + - - +
68A HIS* 3.5 33.2 + - + +
69A VAL* 2.9 25.9 + - - +
222A ARG* 3.5 5.6 - - - +
234A LYS* 1.3 67.8 - - - +
236A LEU* 1.3 67.0 + - - +
237A SER* 4.8 5.9 + - - -
252A SER* 5.0 2.1 - - - -
253A GLU* 3.3 30.1 + - - +
254A ASP* 2.4 35.4 + - - +
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 3.4 11.0 - - + +
76A ALA 4.8 0.2 - - - +
79A ALA* 3.3 34.3 - - + +
80A SER* 3.8 20.0 - - - +
83A ALA* 3.8 14.4 - - + -
215A LEU* 4.0 16.3 - - + +
218A LEU* 3.8 11.6 - - + +
234A LYS 3.2 4.4 + - - -
235A ASN* 1.3 72.3 - - - +
237A SER* 1.3 72.9 + - - +
238A VAL* 4.3 17.0 - - + -
251A TYR 4.2 0.3 - - - +
252A SER* 3.6 0.9 - - - -
253A GLU* 3.2 29.7 + - - +
261A ILE* 3.7 29.8 - - + -
264A VAL* 6.3 0.2 - - + -
265A VAL* 4.9 0.2 - - + -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL 3.1 7.2 + - - -
70A SER* 3.2 23.0 + - - -
71A GLY 3.2 22.0 + - - -
215A LEU* 6.0 0.2 - - - -
235A ASN* 4.8 5.1 + - - -
236A LEU* 1.3 76.1 - - - +
238A VAL* 1.3 65.2 + - - +
239A VAL* 5.6 0.4 - - - -
250A ARG* 4.2 17.0 + - - -
251A TYR 3.2 5.6 - - - -
252A SER* 3.2 25.6 - - - -
298A ILE* 5.0 6.2 - - - +
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Residues in contact with VAL 238 (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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71A GLY 3.3 9.4 - - - +
76A ALA* 4.1 24.7 - - + +
215A LEU* 5.9 1.8 - - + -
236A LEU* 4.3 20.4 - - + -
237A SER* 1.3 79.7 - - - +
239A VAL* 1.3 65.3 + - - +
240A VAL* 4.4 7.4 + - + -
250A ARG* 3.4 4.0 - - - +
251A TYR* 2.8 40.9 + - + +
264A VAL* 3.5 40.6 - - + +
265A VAL* 4.4 14.1 - - + -
268A SER* 4.6 0.7 - - - -
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Residues in contact with VAL 239 (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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70A SER* 5.0 2.0 - - - +
71A GLY 3.3 6.0 + - - +
72A ALA* 3.8 5.9 - - + +
237A SER 5.6 0.2 - - - -
238A VAL* 1.3 79.3 - - - +
240A VAL* 1.3 64.3 - - - +
248A LEU* 3.6 35.4 - - + -
249A GLU 3.2 11.0 - - - +
250A ARG* 4.3 17.9 - - + -
268A SER* 2.6 26.9 + - - -
289A GLY* 3.3 11.6 - - - +
294A ASN* 4.3 4.7 - - - +
296A PRO* 3.7 36.1 - - + -
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Residues in contact with VAL 240 (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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238A VAL* 4.6 7.6 - - + -
239A VAL* 1.3 78.5 - - - +
241A THR* 1.3 66.9 + - - +
248A LEU* 3.4 12.3 - - - +
249A GLU* 2.9 52.8 + - + +
251A TYR* 3.9 16.6 - - + -
264A VAL 4.0 6.5 - - - +
267A TRP* 4.0 10.5 - - + -
268A SER* 3.8 26.2 - - - +
286A ILE* 3.9 16.8 - - + -
287A ALA 3.8 8.1 - - - +
289A GLY* 3.6 7.6 - - - -
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Residues in contact with THR 241 (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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240A VAL* 1.3 78.5 - - - +
242A ASN* 1.3 68.3 + - - +
243A GLN* 3.4 6.1 + - + +
247A GLU 3.7 2.5 - - - +
248A LEU* 3.7 8.4 - - - +
286A ILE* 3.2 8.3 - - - +
287A ALA* 3.0 33.0 + - - -
288A ASP 2.4 27.5 + - - -
289A GLY* 3.6 7.3 - - - -
291A ILE* 4.4 8.8 + - + +
291C ILE* 4.3 19.7 - - + +
292C LEU* 3.6 29.4 - - + +
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Residues in contact with ASN 242 (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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240A VAL* 4.2 1.0 + - - +
241A THR* 1.3 72.2 - - - +
243A GLN* 1.3 52.7 + - - +
244A THR* 3.0 14.6 + - - -
245A LYS* 2.6 43.0 + - + +
246A HIS* 2.6 37.4 + - - -
247A GLU* 2.8 19.2 + - + +
248A LEU* 4.8 0.2 - - - +
249A GLU* 2.9 33.2 + - + +
280A ASN* 3.6 5.7 - - - +
284A GLU* 2.8 28.1 + - - +
285A TYR 3.4 5.2 - - - -
286A ILE* 4.3 7.1 - - - +
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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