Contacts of the strand formed by residues 271 - 277 (chain A) in PDB entry 2K0G
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 ARG 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A ILE 5.9 0.6 + - - -
267A GLU* 4.1 26.5 + - - -
268A PRO 4.9 1.6 + - - -
269A GLY* 5.7 0.2 - - - -
270A ASP* 1.3 95.7 + - - +
272A MET* 1.3 61.7 + - - +
273A PHE* 3.3 35.4 - - + -
297A GLY 3.4 12.0 - - - +
301A LEU* 3.1 13.1 - - - +
307A ARG* 3.7 8.0 + - - +
321A SER* 5.5 5.2 - - - -
322A LEU 3.2 16.8 - - - +
323A HIS* 5.2 0.4 - - - -
324A SER 4.7 0.2 - - - +
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Residues in contact with MET 272 (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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271A ARG* 1.3 73.3 - - - +
273A PHE* 1.3 78.9 + - - +
274A PHE* 3.4 47.3 - - + -
295A PHE* 3.7 4.7 - - + -
296A PHE 2.8 26.7 - - - +
297A GLY 3.0 26.2 - - - +
298A GLU* 3.2 26.5 - - + +
301A LEU* 3.2 4.9 - - + +
320A LEU 3.6 3.6 - - - +
321A SER* 3.6 4.3 - - - -
322A LEU* 3.1 29.5 + - + -
327A PHE* 3.4 28.9 - - + -
341A PHE* 4.1 4.9 - - + -
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Residues in contact with PHE 273 (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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256A VAL* 6.2 0.4 - - + -
262A ILE* 2.8 47.3 - - + -
263A CYS* 4.4 6.3 - - - -
271A ARG* 3.3 47.3 - - + -
272A MET* 1.3 94.7 - - - +
274A PHE* 1.3 67.4 + - - +
295A PHE* 3.4 0.7 - - - -
296A PHE* 2.9 61.9 + + + +
297A GLY* 4.8 0.7 - - - -
307A ARG* 4.0 14.6 - - - -
319A LEU* 4.4 13.9 - - + -
320A LEU 3.5 6.3 - - - -
321A SER* 5.9 5.2 - - - -
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Residues in contact with PHE 274 (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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233A VAL* 4.5 15.3 - - + -
235A LEU* 3.6 17.5 - - + -
236A PHE* 3.2 42.0 - + - -
272A MET* 3.4 49.1 - - + -
273A PHE* 1.3 74.4 - - - +
275A VAL* 1.3 58.9 + - - +
276A VAL* 3.5 1.9 + - - +
294A ALA 3.4 7.2 - - - +
295A PHE* 3.5 17.7 - + + -
296A PHE* 4.1 0.2 - - - -
319A LEU* 2.7 36.0 - - - +
320A LEU* 3.1 33.6 + - + -
321A SER 5.2 0.2 - - - -
322A LEU* 4.0 17.5 - - + -
341A PHE* 4.9 1.8 - + - -
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Residues in contact with VAL 275 (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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233A VAL* 5.4 3.6 - - - +
274A PHE* 1.3 72.6 - - - +
276A VAL* 1.3 63.8 + - - +
277A GLU 4.1 6.5 - - - +
278A GLY 3.6 15.7 - - - +
279A SER* 5.1 1.1 - - - -
280A VAL* 4.2 20.9 - - + -
290A LEU* 5.0 5.2 - - + -
291A GLY* 3.0 31.2 - - - +
292A PRO* 3.4 9.4 - - + -
293A GLY* 2.8 25.8 + - - -
294A ALA* 2.8 14.2 + - + +
296A PHE* 3.4 27.6 - - + -
317A VAL* 4.9 4.9 - - + -
318A SER 4.0 3.4 - - - +
319A LEU* 4.1 5.4 - - + -
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Residues in contact with VAL 276 (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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229A LEU* 3.4 40.2 - - + +
232A ALA* 5.0 13.3 - - + +
233A VAL* 5.6 2.0 - - + -
274A PHE* 3.7 4.3 - - + +
275A VAL* 1.3 77.4 - - - +
277A GLU* 1.3 66.0 + - + +
292A PRO* 3.0 16.9 - - - +
293A GLY 4.6 1.0 + - - +
318A SER* 2.7 28.5 + - - +
319A LEU* 3.9 1.6 - - - -
320A LEU* 3.4 36.3 - - + -
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Residues in contact with GLU 277 (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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275A VAL* 3.8 1.3 - - - -
276A VAL* 1.3 90.4 - - + +
278A GLY* 1.3 64.7 + - - +
292A PRO* 3.9 10.5 - - - +
316A THR 4.4 0.5 - - - +
317A VAL* 3.0 29.4 - - - +
318A SER* 3.2 11.3 + - - +
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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