Contacts of the strand formed by residues 254 - 264 (chain B) in PDB entry 5K7W
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 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A TRP* 5.5 1.8 - - - -
252B GLY 5.5 2.1 + - - +
253B TYR* 1.3 76.1 - - - +
255B ARG* 1.3 68.9 + - - +
256B CYS* 3.2 1.1 + - + -
291B GLY* 3.2 2.6 - - - -
292B ILE* 2.9 67.2 + - + +
293B LYS* 4.3 0.6 - - - +
294B GLY 3.0 41.2 + - - +
295B THR* 4.9 2.2 - - - +
296B VAL 5.3 0.6 - - - +
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Residues in contact with ARG 255 (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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434A GLY* 3.0 28.7 + - - -
435A ARG* 4.3 1.6 - - - +
437A MET* 3.6 13.3 - - - +
438A GLU* 2.8 50.0 + - + +
245B ARG* 3.6 28.0 - - + +
248B LEU* 3.9 23.8 - - + +
253B TYR 4.1 2.2 + - - -
254B ARG* 1.3 73.2 - - - +
256B CYS* 1.3 86.5 + - - +
257B GLU* 3.7 20.9 + - - +
258B ASP* 5.1 1.9 - - - +
289B LEU* 4.5 9.2 - - + -
290B MET 3.5 9.9 - - - +
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Residues in contact with CYS 256 (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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474A HIS* 5.8 0.2 - - - +
475A TRP* 3.5 32.1 - - - +
230B PHE* 4.7 0.2 - - - -
254B ARG* 3.9 2.9 - - + +
255B ARG* 1.3 86.7 + - - +
257B GLU* 1.3 75.5 + - - +
290B MET* 2.8 42.7 + - - -
291B GLY 3.9 0.7 - - - -
292B ILE* 3.9 32.8 - - + -
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Residues in contact with GLU 257 (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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474A HIS* 3.8 2.8 + - - +
475A TRP* 3.0 40.4 + - + +
476A LEU* 3.1 26.0 + - + +
478A HIS* 2.7 34.4 + - - -
255B ARG* 3.7 15.7 + - - +
256B CYS* 1.3 88.3 - - - +
258B ASP* 1.3 64.1 + - - +
259B ILE* 5.1 0.4 - - + -
289B LEU* 3.9 1.0 - - - -
290B MET* 2.9 56.1 + - + +
312B ASP* 4.7 3.1 - - + +
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Residues in contact with ASP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A MET* 6.0 3.8 - - + -
454A GLU* 4.3 2.9 - - - +
480A LYS* 2.7 32.1 + - - +
482A HIS* 3.3 24.3 + - + +
241B LEU* 5.6 0.2 - - - +
245B ARG* 4.7 8.0 + - - +
255B ARG* 5.1 4.5 - - - +
257B GLU* 1.3 77.4 + - - +
259B ILE* 1.3 66.3 + - - +
260B CYS* 3.8 1.0 - - - -
287B HIS* 2.8 43.1 + - - +
288B CYS 3.8 5.2 + - - +
289B LEU* 3.7 20.6 - - + +
312B ASP* 3.6 5.8 + - - +
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Residues in contact with ILE 259 (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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476A LEU* 3.7 31.2 - - + -
232B PHE* 4.0 24.0 - - + -
234B TRP* 4.8 1.3 - - + -
257B GLU* 5.1 1.6 - - + -
258B ASP* 1.3 75.5 - - - +
260B CYS* 1.3 62.5 + - - +
261B TRP 3.8 1.1 + - - +
286B GLU 3.9 0.2 - - - +
287B HIS* 3.7 0.3 - - - -
288B CYS* 2.8 49.8 + - + +
290B MET* 4.9 3.6 - - + -
312B ASP* 3.4 19.1 - - - +
314B ILE* 4.0 29.6 - - + -
330B ILE* 3.8 22.9 - - + -
333B ILE* 4.2 14.8 - - + -
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Residues in contact with CYS 260 (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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456A ILE* 3.9 26.0 - - + -
480A LYS* 3.7 25.6 - - - -
482A HIS* 4.3 0.2 - - - -
258B ASP* 3.6 5.6 + - - -
259B ILE* 1.3 73.4 - - - +
261B TRP* 1.3 60.9 + - - +
262B ILE* 3.6 4.0 + - + -
285B LYS* 4.4 2.7 - - + -
286B GLU 3.4 3.4 - - - +
287B HIS* 3.4 42.8 - - - -
312B ASP 3.0 7.5 + - - -
313B LEU* 3.4 8.7 - - + +
314B ILE 2.9 24.8 + - - +
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Residues in contact with TRP 261 (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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234B TRP* 4.0 20.6 - + + -
259B ILE 3.8 1.8 + - - -
260B CYS* 1.3 69.2 - - - +
262B ILE* 1.3 68.5 + - - +
263B LYS* 3.7 20.5 + - + +
285B LYS* 3.1 5.5 - - - -
286B GLU* 2.8 74.9 + - + +
314B ILE* 3.3 19.1 - - + -
316B THR* 2.8 28.2 + - - -
319B PRO* 3.7 32.1 - - + -
325B GLU 3.6 17.9 - - - -
326B LYS* 4.0 10.8 - - + -
327B PRO* 3.4 38.4 - - + +
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Residues in contact with ILE 262 (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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456A ILE* 3.6 18.8 - - + -
458A VAL* 3.5 24.2 - - + -
502A VAL* 4.2 7.9 - - + -
131B GLN* 3.5 42.4 - - + +
134B ILE* 5.5 0.2 - - + -
260B CYS* 4.2 6.1 - - + +
261B TRP* 1.3 75.7 - - - +
263B LYS* 1.3 61.1 + - - +
264B THR 4.0 0.3 + - - -
284B THR 4.0 3.1 - - - -
285B LYS* 4.1 5.8 - - + -
313B LEU* 3.5 29.6 - - + -
314B ILE 2.8 11.4 + - - +
315B ILE* 3.4 19.9 - - + +
316B THR 3.2 23.9 + - - +
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Residues in contact with LYS 263 (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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129B ARG* 3.0 22.7 + - - +
131B GLN* 2.9 20.8 + - - -
261B TRP* 3.7 49.3 - - + +
262B ILE* 1.3 71.4 - - - +
264B THR* 1.3 61.2 + - - +
283B ARG 5.9 0.7 - - - -
284B THR* 3.0 24.4 + - - +
285B LYS* 4.3 4.4 + - - -
286B GLU* 2.9 33.7 + - - +
316B THR 3.2 4.5 - - - +
318B GLU* 3.4 38.8 + - - +
319B PRO* 4.9 1.9 - - - +
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Residues in contact with THR 264 (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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129B ARG* 4.2 0.7 - - - +
131B GLN* 3.5 33.9 - - + +
132B ASN* 3.2 17.0 - - - +
263B LYS* 1.3 75.2 - - - +
265B ASN* 1.3 61.9 + - - +
266B LYS* 4.3 16.6 + - - +
315B ILE* 3.8 21.1 - - + -
316B THR 2.9 7.3 + - - +
317B GLU* 2.8 35.1 + - - +
318B GLU* 2.9 28.1 + - - +
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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