Contacts of the strand formed by residues 359 - 370 (chain A) in PDB entry 2D7I
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 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A ASN* 5.6 7.1 - - - +
259A LYS 3.3 5.6 + - - -
260A THR* 4.2 19.6 + - + +
261A ILE 2.8 23.6 + - - -
313A GLU* 3.3 36.1 + - - +
353A VAL* 3.2 12.2 + - - +
354A TRP* 3.6 31.2 - - + -
357A GLY 5.4 0.9 - - - +
358A GLY* 1.3 79.7 - - - +
360A MET* 1.3 62.6 + - - +
361A GLU* 3.1 25.9 + - - -
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Residues in contact with MET 360 (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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261A ILE* 3.3 15.0 - - + +
263A CYS* 4.3 10.1 - - - -
313A GLU* 3.5 0.7 - - - -
314A SER* 3.2 29.8 + - - +
315A PRO 3.5 19.1 - - - +
316A VAL* 3.5 3.6 - - - -
317A MET* 3.3 50.0 - - - +
350A SER* 3.1 33.4 - - - +
353A VAL* 4.7 4.9 - - + -
354A TRP* 3.2 24.8 - - + +
359A ARG* 1.3 77.4 - - - +
361A GLU* 1.3 69.8 + - - +
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Residues in contact with GLU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 2.7 53.0 + - - +
257A ASN* 5.2 1.0 - - - +
260A THR* 3.6 17.9 - - + +
261A ILE 2.9 10.1 + - - -
262A VAL* 3.2 1.7 - - + -
263A CYS* 2.7 31.8 + - - +
311A PRO* 4.1 8.2 - - + +
312A PHE 3.4 17.4 - - - +
313A GLU* 4.4 6.9 - - + +
314A SER 4.6 0.9 - - - +
359A ARG* 3.1 26.4 + - - +
360A MET* 1.3 82.7 - - - +
362A ASP* 1.3 63.8 + - - +
363A ILE* 3.1 10.1 - - + +
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Residues in contact with ASP 362 (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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263A CYS* 3.2 27.0 - - - +
264A PRO 4.6 3.9 - - - +
265A MET* 3.4 21.8 - - + +
284A MET 4.1 7.3 + - - +
311A PRO* 3.5 2.8 - - - +
312A PHE* 2.9 47.3 + - + +
314A SER* 3.7 20.7 + - - -
316A VAL 5.5 0.2 - - - +
317A MET* 5.7 1.4 - - - -
361A GLU* 1.3 73.3 - - - +
363A ILE* 1.3 58.8 + - - +
364A PRO* 3.1 11.1 - - - +
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Residues in contact with ILE 363 (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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249A PRO* 3.9 29.4 - - + +
250A LEU* 3.8 7.9 - - + -
253A ARG* 4.9 2.7 - - + -
262A VAL* 3.1 39.9 - - + -
263A CYS 2.8 17.4 + - - +
265A MET* 3.3 5.8 + - - +
309A SER 5.8 0.2 - - - +
311A PRO* 4.7 19.7 - - + -
361A GLU* 3.1 15.3 - - + +
362A ASP* 1.3 73.6 - - - +
364A PRO* 1.3 67.4 - - + +
365A CYS* 3.8 6.5 - - + +
366A SER* 2.9 44.4 + - - +
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Residues in contact with PRO 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 4.7 2.8 - - - +
132A HIS* 5.0 4.3 + - + -
135A CYS* 4.2 5.3 - - - -
265A MET* 3.4 16.3 - - + +
283A ALA* 5.1 4.0 - - + -
308A PRO 4.1 10.3 - - - +
309A SER* 3.7 24.2 - - - +
310A ASP 3.6 25.6 - - - +
311A PRO* 4.1 0.2 - - + -
312A PHE* 3.6 20.0 - - + -
362A ASP 3.1 13.5 - - - +
363A ILE* 1.3 83.3 - - + +
365A CYS* 1.3 58.3 + - - +
366A SER 3.2 1.4 + - - -
367A ARG* 3.6 25.1 + - - +
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Residues in contact with CYS 365 (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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131A ARG* 3.6 22.1 + - - +
135A CYS* 2.0 56.3 - - + +
138A LYS* 4.4 6.3 - - - -
140A TYR* 3.7 24.0 - - - +
244A VAL 4.6 0.5 - - - +
245A ASN* 3.7 13.8 + - - +
249A PRO* 4.1 3.7 - - + +
309A SER* 3.7 20.2 - - - -
363A ILE* 3.0 10.2 + - + +
364A PRO* 1.3 78.2 - - - +
366A SER* 1.3 59.0 + - - +
367A ARG* 4.0 0.8 + - - -
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Residues in contact with SER 366 (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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246A TRP* 2.6 35.8 + - - +
249A PRO* 3.9 2.5 - - - -
250A LEU* 3.4 14.5 - - - +
264A PRO* 3.2 18.3 - - - +
265A MET 2.7 24.4 + - - -
363A ILE* 2.9 23.8 + - - +
365A CYS* 1.3 77.6 - - - +
367A ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 367 (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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130A ILE* 3.6 25.2 + - - +
131A ARG* 4.0 30.1 - - + +
132A HIS 5.4 0.4 - - - +
243A ASN* 2.9 38.1 + - + +
244A VAL 5.7 0.6 + - - -
246A TRP* 3.9 5.9 - - - +
264A PRO* 4.3 0.2 - - - -
265A MET* 3.4 26.4 - - + +
267A ASP* 2.6 44.2 + - - +
276A TYR* 4.0 3.6 - - - +
278A THR* 2.9 14.6 + - - -
282A ASP* 2.8 36.0 + - - -
364A PRO* 3.6 18.4 + - - +
365A CYS 4.0 1.2 + - - -
366A SER* 1.3 80.0 + - - +
368A VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 368 (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 LEU* 4.9 5.2 - - + -
240A CYS* 3.7 17.5 - - + -
241A GLU 3.7 14.6 - - - +
242A ALA* 4.0 5.8 - - + +
246A TRP* 3.9 25.6 - - + -
264A PRO* 3.8 22.0 - - + -
265A MET 3.1 6.7 + - - +
266A ILE* 3.5 7.5 - - - +
267A ASP 2.8 22.1 + - - -
276A TYR* 4.1 2.7 - - - -
321A LEU* 3.8 21.8 - - + -
367A ARG* 1.3 80.8 - - - +
369A GLY* 1.3 76.1 + - - +
370A HIS* 4.8 0.2 - - - +
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Residues in contact with GLY 369 (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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240A CYS* 3.1 10.6 - - - +
241A GLU 2.9 30.8 + - - -
267A ASP 3.4 7.4 - - - -
269A ILE* 3.4 15.0 - - - -
276A TYR* 3.5 25.8 - - - -
368A VAL* 1.3 76.6 - - - +
370A HIS* 1.3 58.9 + - - +
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Residues in contact with HIS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 3.3 13.5 + - + -
239A HIS* 3.3 16.2 - + - -
240A CYS* 3.9 8.3 - - - -
266A ILE* 3.6 22.0 - - + -
267A ASP 2.6 11.7 + - - +
268A VAL* 3.5 2.9 - - - -
269A ILE* 2.9 22.6 + - - +
321A LEU* 4.5 2.7 - - + -
369A GLY* 1.3 73.9 - - - +
371A ILE* 1.3 81.3 + - - +
372A TYR* 3.6 29.9 + + + -
702A NGA 3.6 22.0 - - + +
705A UDP 3.3 8.6 + - - -
706A MN 2.3 35.7 + - - -
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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