Contacts of the strand formed by residues 248 - 262 (chain A) in PDB entry 1SR5
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 SER 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LYS* 3.9 31.6 + - - +
237A GLU 3.6 6.1 - - - -
238A LEU* 5.0 5.6 - - - +
247A CYS* 1.3 73.6 - - - +
249A ALA* 1.3 58.1 + - - +
430A CYS* 2.9 15.5 - - - +
431A VAL* 3.2 25.5 + - - +
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Residues in contact with ALA 249 (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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236A LYS* 3.2 26.6 - - - +
237A GLU 3.0 16.7 + - - +
239A PHE* 4.2 16.8 - - + -
247A CYS 3.4 0.2 + - - -
248A SER* 1.3 74.3 - - - +
250A SER* 1.3 64.5 + - - +
251A MET* 3.7 6.0 - - + -
321A PRO* 4.8 4.3 - - + -
429A PRO* 4.5 9.4 - - + -
430A CYS* 3.7 25.8 - - + +
431A VAL* 4.4 2.7 - - - +
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Residues in contact with SER 250 (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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234A THR* 3.7 8.5 - - - +
235A ARG 4.1 2.9 - - - -
236A LYS* 4.7 1.8 - - - +
249A ALA* 1.3 72.4 - - - +
251A MET* 1.3 56.8 + - - +
321A PRO* 3.4 4.4 - - - +
322A ARG* 2.9 76.0 + - - +
429A PRO 5.3 0.6 + - - -
430A CYS* 5.2 0.2 - - - +
431A VAL* 4.6 15.8 - - - +
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Residues in contact with MET 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASN 4.3 1.4 - - - +
234A THR* 3.4 6.2 - - - +
235A ARG* 2.8 42.6 + - + +
237A GLU* 3.7 44.0 - - + +
238A LEU 5.1 1.1 - - - +
239A PHE* 4.7 4.9 - - + -
249A ALA* 3.4 6.5 + - + +
250A SER* 1.3 70.5 + - - +
252A MET* 1.3 68.1 + - - +
253A TYR* 4.8 1.0 - - + +
319A HIS* 3.5 13.9 - - + +
320A MET* 3.1 40.4 - - - +
321A PRO* 3.4 10.3 - - + -
403A LYS* 6.5 0.2 - - + -
404A ALA 3.5 17.9 - - - +
405A ASN* 4.0 15.3 - - + -
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Residues in contact with MET 252 (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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225A TRP* 4.6 2.0 - - - +
229A PHE* 3.0 35.4 - - + -
234A THR* 3.8 12.1 - - + +
250A SER 4.0 0.2 + - - -
251A MET* 1.3 76.2 - - - +
253A TYR* 1.3 62.2 + - - +
319A HIS* 3.3 4.5 - - - -
320A MET* 2.8 69.5 + - + +
321A PRO 3.3 13.7 - - - +
322A ARG* 3.8 17.9 - - + -
375A VAL* 3.6 19.7 - - + -
376A ASN* 3.6 5.4 - - - +
377A GLU* 3.4 35.4 - - + -
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Residues in contact with TYR 253 (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 PHE* 3.9 8.7 - - - -
230A SER* 4.8 8.1 + - - +
233A ASN* 3.9 48.4 + - + +
234A THR* 4.7 2.2 + - - -
235A ARG* 3.1 29.6 - - - +
251A MET* 4.8 1.8 - - + +
252A MET* 1.3 78.8 - - - +
254A GLN* 1.3 83.9 + - - +
255A GLU* 3.5 28.1 + - + +
317A VAL* 3.0 32.0 - - + +
318A VAL 3.1 16.4 - - - +
319A HIS* 4.0 16.8 - + - +
399A ARG* 5.8 0.3 + - - -
146C GLU 5.5 2.8 + - - -
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Residues in contact with GLN 254 (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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227A SER* 2.9 37.9 + - - +
228A LYS 4.1 2.9 - - - +
229A PHE* 3.9 32.9 - - + -
230A SER* 5.6 2.5 - - - +
233A ASN* 6.0 1.1 - - - +
253A TYR* 1.3 88.7 - - - +
255A GLU* 1.3 69.4 + - - +
258A PHE* 2.5 41.2 - - + -
317A VAL* 3.7 0.2 - - - -
318A VAL* 2.8 33.2 + - + +
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Residues in contact with GLU 255 (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 TYR* 3.5 26.5 + - + +
254A GLN* 1.3 87.0 + - - +
256A GLY* 1.3 60.1 + - - +
315A MET* 5.5 1.7 - - + +
316A LEU 3.2 7.0 - - - +
317A VAL* 4.2 10.3 - - + -
390A ILE* 3.8 44.4 - - + +
399A ARG* 4.1 28.9 + - - -
146C GLU 5.7 0.7 - - - +
192C GLU* 4.8 5.8 - - - +
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Residues in contact with GLY 256 (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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227A SER* 6.1 0.4 - - - -
255A GLU* 1.3 76.6 - - - +
257A LYS* 1.3 60.7 + - - -
258A PHE* 3.6 17.3 + - - -
314A MET 3.6 0.2 - - - +
315A MET* 3.5 15.8 - - - +
316A LEU* 2.8 39.4 + - - +
389A VAL* 5.7 1.3 - - - -
390A ILE* 4.5 4.3 - - - -
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Residues in contact with LYS 257 (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 GLY* 1.3 70.3 - - - -
258A PHE* 1.3 74.8 + - - +
313A GLU* 3.6 46.2 + - + +
314A MET* 2.9 15.9 - - - +
315A MET* 3.8 14.9 - - - +
389A VAL* 5.5 11.6 - - + +
60C PRO* 4.1 37.9 + - - +
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Residues in contact with PHE 258 (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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227A SER* 4.0 14.8 - - - -
229A PHE* 6.0 0.4 - + - -
254A GLN* 2.5 39.7 - - + -
256A GLY* 3.6 18.2 + - - -
257A LYS* 1.3 93.1 - - - +
259A ARG* 1.3 64.7 + - - +
260A TYR 3.1 2.4 + - - -
270A LEU* 3.8 10.3 - - + -
271A GLU 4.1 4.0 - - - +
272A LEU* 4.1 18.6 - - + -
273A PRO* 4.8 15.7 - - + -
313A GLU* 4.4 2.0 - - - -
314A MET* 3.0 29.4 + - - +
316A LEU* 3.1 30.7 - - + +
318A VAL* 3.5 25.4 - - + -
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Residues in contact with ARG 259 (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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258A PHE* 1.3 71.2 - - - +
260A TYR* 1.3 58.3 + - - +
270A LEU* 3.8 0.7 - - - +
271A GLU* 3.1 53.7 + - + +
311A LEU* 3.0 48.1 + - + +
312A GLU* 3.3 10.1 - - - +
313A GLU* 3.7 31.2 - - + +
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Residues in contact with TYR 260 (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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258A PHE 3.1 4.6 + - - +
259A ARG* 1.3 75.7 - - - +
261A ARG* 1.3 88.2 + - - +
262A ARG* 2.6 42.2 + - + +
268A GLN* 2.9 26.2 + - + -
269A VAL 3.1 18.2 - - - +
270A LEU* 4.2 11.7 - - + -
311A LEU* 3.8 3.8 - - - -
312A GLU 2.8 28.3 + - - +
314A MET* 3.8 28.7 - - + +
316A LEU* 3.4 31.2 - - + -
400A VAL* 3.5 26.2 - - + +
402A PHE* 4.7 2.2 - + - -
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Residues in contact with ARG 261 (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 TYR* 1.3 90.3 - - - +
262A ARG* 1.3 67.5 + - - +
263A VAL* 3.5 20.1 + - + +
269A VAL* 2.9 31.6 + - + +
307A TRP 5.1 0.2 - - - +
310A GLU* 3.0 41.6 + - + +
311A LEU* 3.5 18.6 - - + -
312A GLU* 4.0 19.3 - - - +
314A MET* 4.9 9.8 - - - +
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Residues in contact with ARG 262 (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 TYR* 2.6 43.2 + - + +
261A ARG* 1.3 79.1 - - - +
263A VAL* 1.3 69.4 - - - +
266A GLY* 4.9 16.6 + - - -
267A THR 3.9 10.3 - - - +
268A GLN* 2.9 28.9 + - + +
287A LYS* 6.3 0.6 - - - +
314A MET* 6.0 0.2 - - - +
400A VAL* 4.2 9.3 - - - +
401A THR 5.0 0.6 + - - -
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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