Contacts of the strand formed by residues 249 - 260 (chain A) in PDB entry 3KYB
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 TYR 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A PRO* 6.4 2.0 - - + -
237A ASP* 6.0 1.1 - - - -
247A LEU* 3.5 18.9 + - + -
248A GLY* 1.3 76.1 - - - -
250A ARG* 1.3 60.6 + - - +
305A ALA* 3.9 2.1 - - - +
306A CYS* 2.9 43.3 + - + +
312A PRO* 3.3 31.9 - - + -
313A TYR 3.7 16.6 - - - -
314A TYR 3.2 23.8 - - - -
315A PRO* 3.4 16.7 - - + +
316A ILE* 3.5 15.7 - - - +
343A ARG* 3.8 17.2 + - + +
344A LEU* 3.7 20.4 + - + +
347A TYR* 3.5 33.1 - + - -
348A ARG 4.9 0.9 + - - -
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Residues in contact with ARG 250 (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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158A LYS 3.4 14.8 + - - -
159A GLN 2.4 31.9 - - - +
160A TRP* 3.4 21.8 + - - +
161A GLY* 3.5 16.0 + - - +
249A TYR* 1.3 76.1 - - - +
251A THR* 1.3 60.2 + - - +
303A SER* 3.3 23.3 + - - +
304A ARG* 3.4 24.1 + - - +
305A ALA* 3.4 25.3 - - - +
306A CYS* 4.0 2.0 - - - -
313A TYR* 3.2 22.7 + - - +
314A TYR* 2.7 31.1 + - + +
316A ILE* 4.4 12.0 - - + +
392A FMN 4.3 17.7 - - + -
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Residues in contact with THR 251 (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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250A ARG* 1.3 75.4 - - - +
252A LEU* 1.3 75.1 + - - +
253A ASP* 4.8 0.2 - - - +
303A SER* 3.5 6.1 + - - -
304A ARG* 2.7 61.5 + - + +
305A ALA 3.9 3.1 - - - +
306A CYS* 3.9 6.5 - - - +
310A ASP* 3.6 31.8 - - + +
311A ILE 2.4 28.7 + - - -
313A TYR* 3.6 9.9 - - - -
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Residues in contact with LEU 252 (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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250A ARG* 6.1 0.2 - - + -
251A THR* 1.3 90.3 + - - +
253A ASP* 1.3 65.2 + - - +
254A PHE* 3.8 36.3 + - + -
279A THR* 5.4 4.0 - - + +
280A ARG* 5.8 1.8 - - - +
301A GLU* 4.9 11.2 - - + +
302A TYR 3.1 17.3 - - - +
303A SER* 4.0 15.9 - - - +
313A TYR* 3.3 23.5 + - + -
314A TYR* 3.7 24.2 - - + +
391A FAD 3.7 29.8 - - + -
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Residues in contact with ASP 253 (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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251A THR* 4.8 0.3 - - - +
252A LEU* 1.3 76.7 - - - +
254A PHE* 1.3 62.7 + - - +
255A LYS* 6.2 0.4 - - + -
300A LYS 3.5 2.1 - - - +
301A GLU* 3.4 4.7 - - - -
302A TYR* 2.8 50.9 + - + +
304A ARG* 2.9 50.5 + - - +
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Residues in contact with PHE 254 (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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56A VAL 4.0 13.5 - - - +
57A TYR* 3.9 13.9 - + - -
58A GLY* 3.9 20.6 - - - -
252A LEU* 3.8 34.8 - - + -
253A ASP* 1.3 74.9 - - - +
255A LYS* 1.3 59.0 + - - +
256A LYS* 3.6 3.2 + - - +
299A TYR* 3.9 26.0 - + + -
300A LYS 3.6 2.9 - - - -
301A GLU* 3.6 44.2 - - + -
313A TYR* 3.4 28.5 - + - -
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Residues in contact with LYS 255 (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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253A ASP* 3.8 2.3 + - + -
254A PHE* 1.3 69.4 - - - +
256A LYS* 1.3 68.9 + - - +
257A PHE* 3.7 8.1 + - + -
298A CYS 3.8 0.2 - - - +
299A TYR* 3.4 5.0 - - - -
300A LYS* 2.8 64.6 + - + +
302A TYR* 3.3 38.1 + - + +
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Residues in contact with LYS 256 (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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47A ASP* 2.8 28.3 + - - +
254A PHE 3.6 4.6 + - - +
255A LYS* 1.3 80.7 - - - +
257A PHE* 1.3 65.2 + - - +
258A ILE* 3.9 23.5 - - + +
297A VAL* 4.1 16.8 - - + -
298A CYS 3.5 4.9 - - - -
299A TYR* 3.4 31.8 + - + +
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Residues in contact with PHE 257 (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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255A LYS* 3.9 13.7 - - + -
256A LYS* 1.3 75.2 - - - +
258A ILE* 1.3 71.9 + - - +
259A TYR* 5.0 1.6 - + + -
263A TYR* 3.5 52.5 - + - -
281A ILE* 4.0 5.6 - - + -
296A SER 3.7 0.2 - - - +
297A VAL* 3.7 3.3 - - - +
298A CYS* 2.8 66.5 + - + +
299A TYR 4.4 0.7 - - - -
300A LYS* 3.8 40.6 - - + -
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Residues in contact with ILE 258 (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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47A ASP* 4.2 13.9 - - - +
49A GLU* 3.7 24.7 - - + +
50A THR* 4.0 11.4 - - + -
256A LYS* 3.9 29.8 - - + +
257A PHE* 1.3 85.5 - - - +
259A TYR* 1.3 67.2 - - - +
260A GLN* 3.9 24.7 - - + +
296A SER 3.2 11.0 - - - +
297A VAL* 4.4 7.0 - - + -
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Residues in contact with TYR 259 (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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257A PHE* 4.3 3.3 + + + -
258A ILE* 1.3 77.5 - - - +
260A GLN* 1.3 74.4 + - - +
261A GLY 3.4 9.4 + - - -
262A ASP 3.7 18.1 + - - -
263A TYR* 3.6 52.9 - + + -
295A GLY* 3.6 0.9 - - - -
296A SER* 2.8 36.6 + - - +
298A CYS* 5.0 2.5 - - - -
113B SER* 5.6 0.7 + - - -
115B ASP* 2.5 36.6 + - - +
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Residues in contact with GLN 260 (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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49A GLU* 3.3 26.5 + - - +
50A THR* 5.2 0.2 - - - +
258A ILE* 3.9 16.5 - - + +
259A TYR* 1.3 86.1 - - - +
261A GLY* 1.3 57.1 + - - +
294A ASP* 3.7 4.8 - - - +
295A GLY* 3.6 20.0 + - - -
115B ASP* 4.7 2.9 - - - +
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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