Contacts of the strand formed by residues 268 - 275 (chain A) in PDB entry 4CKG
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 MET 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PRO* 3.8 31.6 - - + +
258A SER 4.4 3.1 - - - +
259A LEU* 4.3 16.6 - - + +
260A ARG* 3.9 0.4 - - - +
266A LEU* 4.2 6.7 - - + +
267A VAL* 1.4 76.2 - - - +
269A GLU* 1.3 68.1 + - - +
289A THR* 3.4 2.5 - - - +
290A ILE* 2.9 42.0 + - + +
350A LEU* 4.4 11.0 - - + -
351A TRP* 3.7 54.9 - - + +
354A ALA* 3.9 28.5 - - + -
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Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PRO* 3.7 18.2 - - - +
258A SER* 4.4 4.2 + - - +
260A ARG* 2.6 47.1 + - - -
267A VAL* 5.1 0.7 - - - +
268A MET* 1.3 75.2 - - - +
270A GLY* 1.4 58.5 + - - +
287A TRP* 3.7 26.8 - - + +
288A PHE 3.3 6.1 - - - +
289A THR* 3.5 25.6 - - + +
351A TRP* 4.2 4.7 - - - -
15B PRO* 4.2 20.4 - - + +
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Residues in contact with GLY 270 (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 PRO* 4.9 4.3 - - - -
269A GLU* 1.4 74.7 - - - +
271A HIS* 1.3 65.5 + - - -
287A TRP* 3.5 13.1 - - - +
288A PHE* 3.0 30.6 + - - +
347A LEU* 6.3 0.9 - - - -
351A TRP* 3.6 17.1 - - - -
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Residues in contact with HIS 271 (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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270A GLY* 1.3 76.6 - - - -
272A LEU* 1.3 73.6 + - - +
285A ARG* 3.6 38.0 + - + +
286A ARG 3.4 10.8 - - - +
287A TRP* 3.5 44.9 - + + +
342A ALA* 5.2 0.5 - - - -
343A ASP* 4.2 10.8 + - - +
347A LEU* 5.5 5.7 - - - +
351A TRP* 4.6 3.6 + - - -
13B ASP* 5.7 4.9 - - - -
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Residues in contact with LEU 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 HIS* 1.3 80.0 - - - +
273A PHE* 1.3 70.3 + - - +
274A LYS 4.1 0.4 + - - -
285A ARG* 3.2 27.8 - - - +
286A ARG 3.3 10.8 + - - +
288A PHE* 3.9 31.2 - - + -
329A PHE* 4.1 18.4 - - + -
340A LEU* 4.3 14.8 - - + -
341A GLN 3.4 19.7 - - - +
342A ALA* 3.7 22.7 - - + +
343A ASP* 5.5 0.2 - - - -
351A TRP* 3.9 43.5 - - + -
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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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272A LEU* 1.3 72.6 - - - +
274A LYS* 1.4 58.6 + - - +
283A TRP* 3.6 24.7 - - + -
284A SER* 3.5 9.4 - - - +
285A ARG* 3.0 62.6 - - + -
325A ARG* 5.0 1.8 - - - -
340A LEU* 3.4 5.2 - - - +
341A GLN* 2.7 49.8 + - + +
343A ASP* 3.6 9.0 - - - -
138B LEU 3.6 15.9 - - - -
139B THR* 3.8 25.8 - - + -
142B ALA* 3.4 26.7 - - + -
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Residues in contact with LYS 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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272A LEU 4.1 0.2 + - - -
273A PHE* 1.4 74.0 - - - +
275A ARG* 1.3 68.5 + - - +
276A ALA* 5.3 11.7 - - - +
282A THR 3.8 1.6 - - - +
283A TRP* 3.5 7.4 - - - -
284A SER* 2.8 35.8 + - - +
286A ARG* 4.6 9.5 - - + +
288A PHE* 3.9 26.2 - - + -
297A TYR* 4.2 37.3 + - + -
308A VAL* 5.1 5.8 - - + -
338A CYS* 4.7 14.3 - - + +
339A LEU 3.4 5.2 - - - +
340A LEU* 3.8 20.0 - - + -
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Residues in contact with ARG 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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274A LYS* 1.3 78.4 - - - +
276A ALA* 1.4 70.1 + - - +
281A LYS* 4.0 33.1 + - + +
282A THR* 3.5 32.8 - - - +
283A TRP* 3.6 42.8 - - + +
324A GLU* 2.5 44.2 + - - -
338A CYS* 3.9 2.4 - - - +
339A LEU* 2.9 60.0 + - + +
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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