Contacts of the strand formed by residues 296 - 307 (chain A) in PDB entry 2OKC
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 LEU 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A LEU* 3.9 12.0 - - - +
253A VAL 3.8 12.1 - - - +
254A ASP 4.1 1.6 - - - +
256A ILE* 3.7 27.4 - - + +
292A MSE 3.5 4.2 + - - +
293A MSE 3.6 2.1 + - - +
294A LEU 3.4 1.4 - - - -
295A MSE 1.3 78.7 - - - +
297A LYS* 1.3 69.1 + - - +
300A GLY 4.0 15.7 - - - +
301A ARG* 3.5 36.6 - - - +
302A ALA* 4.3 1.6 - - + -
328A PHE* 4.4 3.1 - - + -
353A PHE* 3.8 30.1 - - + -
355A LYS* 3.3 34.1 + - + +
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Residues in contact with LYS 297 (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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173A THR* 4.8 2.6 + - - +
252A LEU* 4.0 31.6 - - + +
253A VAL* 2.9 23.4 + - - +
254A ASP* 3.0 37.5 + - - +
295A MSE 3.7 0.8 + - - -
296A LEU* 1.3 76.4 - - - +
298A THR* 1.3 68.7 + - - +
299A GLY 3.4 0.3 + - - -
300A GLY* 3.0 20.8 + - - +
355A LYS* 3.4 11.6 - - - +
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Residues in contact with THR 298 (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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252A LEU* 5.5 1.2 - - - +
297A LYS* 1.3 80.5 - - - +
299A GLY* 1.3 62.0 + - - +
300A GLY 3.5 1.6 + - - -
355A LYS* 4.1 20.4 - - - +
356A GLY* 4.4 12.6 - - - -
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Residues in contact with GLY 299 (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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298A THR* 1.3 73.9 - - - +
300A GLY* 1.3 64.1 + - - +
301A ARG* 5.0 5.5 + - - +
354A SER* 4.6 5.7 - - - -
355A LYS 2.8 19.7 + - - -
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Residues in contact with GLY 300 (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 VAL 4.4 1.8 - - - -
254A ASP* 3.2 19.5 - - - -
296A LEU* 4.0 10.7 - - - +
297A LYS* 3.0 18.4 + - - +
298A THR 3.2 2.8 + - - -
299A GLY* 1.3 79.1 - - - +
301A ARG* 1.3 58.9 + - - -
354A SER* 3.1 4.3 - - - -
355A LYS 2.9 25.0 + - - -
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Residues in contact with ARG 301 (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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166A ILE* 2.8 49.0 + - + +
167A ASN 3.3 12.3 + - - -
168A PRO* 3.6 4.8 - - - +
169A GLN* 5.2 1.0 - - - +
172A GLU* 2.9 40.4 + - - -
254A ASP* 2.9 13.0 + - - +
255A VAL* 3.2 25.0 - - + +
256A ILE 2.9 22.7 + - - +
296A LEU* 3.5 6.6 - - - +
299A GLY 5.0 5.1 + - - +
300A GLY* 1.3 74.4 - - - +
302A ALA* 1.3 60.4 + - - +
331A HIS* 5.8 3.1 - - - +
353A PHE 3.2 11.4 - - - +
354A SER* 4.3 9.0 - - - -
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Residues in contact with ALA 302 (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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166A ILE* 3.8 6.8 - - - +
256A ILE* 3.2 22.9 - - + +
292A MSE 5.9 0.4 - - + -
296A LEU* 4.3 5.2 - - + -
301A ARG* 1.3 75.7 - - - +
303A ALA* 1.3 60.0 + - - +
304A VAL* 4.4 7.2 - - + -
351A LEU 3.6 1.0 - - - +
352A PHE* 3.1 6.9 - - - +
353A PHE* 2.8 65.6 + - + +
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Residues in contact with ALA 303 (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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162A MSE 3.3 21.0 - - + +
166A ILE* 3.6 15.6 - - + +
256A ILE 2.9 6.5 + - - -
257A LEU* 3.4 11.2 - - + -
258A ALA 3.1 21.1 + - - -
302A ALA* 1.3 71.1 - - - +
304A VAL* 1.3 62.4 + - - +
350A VAL* 4.3 0.7 - - + -
351A LEU 3.3 6.1 - - - -
352A PHE* 3.6 31.4 - - + -
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Residues in contact with VAL 304 (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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162A MSE 3.7 0.8 - - - +
256A ILE* 4.2 9.6 - - + -
258A ALA* 3.2 13.5 - - + +
260A PRO* 5.0 0.4 - - + -
289A LEU* 5.0 0.7 - - + -
292A MSE 3.6 39.0 - - + -
302A ALA* 4.4 6.5 - - + -
303A ALA* 1.3 82.3 - - - +
305A VAL* 1.3 64.1 + - - +
306A LEU* 3.7 25.0 + - + +
349A ASN 3.6 0.7 - - - +
350A VAL* 3.3 4.8 - - - +
351A LEU* 3.0 42.2 + - + +
353A PHE* 4.2 15.7 - - + -
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Residues in contact with VAL 305 (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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154A THR* 5.2 0.4 - - + -
158A LEU* 4.4 8.5 - - + -
162A MSE 3.7 27.4 - - + -
184A PHE* 4.5 2.0 - - + -
258A ALA 2.9 16.3 + - - +
259A ASN* 3.5 32.3 - - + +
260A PRO* 3.0 23.0 - - - +
262A PHE* 3.7 19.9 - - + -
304A VAL* 1.3 71.1 - - - +
306A LEU* 1.3 64.2 + - - +
336A LEU* 4.3 4.0 - - + -
341A PHE* 4.0 15.7 - - + -
348A ALA* 4.1 6.5 - - + -
349A ASN 3.2 10.8 - - - +
350A VAL* 4.4 4.5 - - + -
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Residues in contact with LEU 306 (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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260A PRO* 4.2 17.5 - - + -
262A PHE* 4.5 3.4 - - - -
285A GLN* 4.0 23.8 - - + +
289A LEU* 3.9 23.8 - - + -
292A MSE 4.7 4.3 - - + -
304A VAL* 3.7 24.1 + - + -
305A VAL* 1.3 81.7 - - - +
307A PRO* 1.3 80.5 - - + +
310A VAL* 4.1 20.2 - - + -
348A ALA* 3.4 2.9 - - - -
349A ASN* 2.8 38.5 + - - +
351A LEU* 4.3 18.4 - - + -
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Residues in contact with PRO 307 (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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262A PHE* 4.3 20.1 - - + +
285A GLN* 3.9 33.0 - - + +
305A VAL 4.8 0.2 - - - +
306A LEU* 1.3 96.1 - - + +
308A ASP* 1.3 67.2 + - - +
309A ASN* 4.2 11.7 - - + +
310A VAL* 3.1 32.3 + - + +
311A LEU* 4.0 2.1 + - - +
346A VAL* 5.9 1.1 - - + -
347A LYS 3.2 13.7 - - - +
348A ALA* 4.2 1.6 - - + -
349A ASN* 3.5 3.3 + - - -
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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