Contacts of the strand formed by residues 283 - 291 (chain B) 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 TRP 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLU* 4.2 13.9 - - - +
273B PHE* 4.1 15.0 - - + -
274B LYS* 3.2 30.5 - - - -
275B ARG* 3.4 53.6 - - + +
282B THR* 1.4 80.9 + - - +
284B SER* 1.4 58.9 + - - +
325B ARG* 3.2 57.7 - - + +
339B LEU* 3.7 24.7 - - + -
340B LEU* 4.7 2.0 - - - -
341B GLN* 3.4 34.5 - - + -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 3.8 9.0 - - - -
274B LYS* 2.8 51.3 + - - +
276B ALA* 5.1 8.1 - - - -
282B THR 4.4 5.4 - - - -
283B TRP* 1.4 76.5 - - - +
285B ARG* 1.4 61.7 + - - +
286B ARG* 3.5 26.0 + - - +
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Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 3.8 26.6 - - - +
163A ARG* 5.1 2.6 - - - +
254B GLU* 4.7 3.8 + - - -
271B HIS* 3.5 45.0 + - + +
272B LEU* 3.4 10.8 - - - +
273B PHE* 3.0 50.8 - - + +
284B SER* 1.4 72.4 + - - +
286B ARG* 1.3 89.7 + - - +
341B GLN 5.3 0.8 + - - -
342B ALA* 5.7 0.2 - - - +
343B ASP* 2.5 45.0 + - - -
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B HIS* 3.7 6.0 - - - +
272B LEU 2.9 32.7 + - - +
274B LYS* 4.4 13.9 - - + -
284B SER* 3.5 20.8 + - - +
285B ARG* 1.3 98.8 + - - +
287B TRP* 1.4 62.1 + - - +
288B PHE* 3.3 15.3 - - + -
297B TYR* 3.8 31.5 - - + -
298B GLN 3.8 15.8 + - - +
299B LYS* 4.8 9.8 + - - +
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Residues in contact with TRP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 5.5 10.5 - - + -
13A ASP 5.7 0.2 - - - -
14A SER* 4.3 17.0 - - - -
15A PRO* 3.4 34.5 - - + -
269B GLU* 3.5 39.8 - - + +
270B GLY* 3.8 20.9 - - - -
271B HIS* 3.5 39.3 - + - +
286B ARG* 1.4 74.8 - - - +
288B PHE* 1.3 62.4 + - - +
289B THR* 4.0 10.9 + - - -
297B TYR* 3.6 1.4 - - - -
298B GLN* 2.9 60.7 + - + +
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B GLU* 3.2 2.6 - - - -
270B GLY 2.8 36.9 + - - +
272B LEU* 3.5 48.7 - - + -
274B LYS* 4.3 20.2 - - + -
286B ARG* 3.3 25.4 - - + -
287B TRP* 1.3 73.6 - - - +
289B THR* 1.4 61.7 + - - +
295B LEU* 3.9 22.7 - - + -
296B VAL 3.5 7.9 - - - -
297B TYR* 3.5 25.1 - + + -
308B VAL* 3.7 16.2 - - + -
338B CYS* 5.1 1.8 - - - -
340B LEU* 3.4 22.0 - - + -
351B TRP* 3.6 8.4 - - + -
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B VAL* 4.9 6.5 - - + -
268B MET 3.5 6.3 - - - +
269B GLU* 3.4 18.9 - - + +
287B TRP* 4.0 9.9 + - - -
288B PHE* 1.4 74.0 - - - +
290B ILE* 1.4 68.2 + - - +
291B GLN* 3.3 35.4 + - + +
294B GLN 3.9 0.7 - - - +
295B LEU* 3.6 4.7 - - - -
296B VAL* 3.0 43.7 + - - +
298B GLN* 6.1 0.3 - - - +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B LEU* 5.2 2.7 - - + -
266B LEU 4.8 7.6 - - - +
267B VAL* 3.5 9.4 - - - +
268B MET* 2.8 44.2 + - + +
289B THR* 1.4 71.2 - - - +
291B GLN* 1.3 65.7 + - - +
293B ASN 5.8 0.9 - - - +
294B GLN 3.4 4.5 - - - +
295B LEU* 3.8 9.2 - - + -
312B LEU* 3.7 26.9 - - + -
351B TRP* 3.7 34.5 - - + -
354B ALA* 3.6 33.9 - - + +
355B VAL* 4.7 6.5 - - + +
358B SER* 3.8 13.2 - - - +
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B LEU 4.6 6.7 - - - -
267B VAL* 4.6 13.7 - - + -
289B THR* 3.3 28.2 - - + +
290B ILE* 1.3 74.4 - - - +
292B SER* 1.3 70.6 + - - +
293B ASN 3.3 3.1 - - - -
294B GLN* 3.1 24.1 + - + +
296B VAL* 4.6 16.3 - - + +
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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