Contacts of the helix formed by residues 310 - 321 (chain A) in PDB entry 1J1C
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 PRO 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A VAL* 4.2 37.2 - - + -
159A LYS* 6.1 1.3 - - - -
251A LEU* 5.1 1.8 - - + -
306A ARG* 4.7 3.4 - - - +
308A ARG 3.3 6.7 - - - +
309A THR* 1.3 89.2 - - + +
311A PRO* 1.3 74.3 - - + +
312A GLU* 3.2 3.4 - - + +
313A ALA* 2.9 31.6 + - + +
314A ILE* 3.3 6.1 + - - +
339A PHE* 4.8 6.1 - - + -
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Residues in contact with PRO 311 (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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309A THR 3.4 6.5 - - - +
310A PRO* 1.3 86.4 - - + +
312A GLU* 1.3 63.2 + - + +
314A ILE* 3.2 12.4 + - + +
315A ALA* 2.9 30.2 + - - +
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Residues in contact with GLU 312 (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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310A PRO* 3.1 4.8 + - + +
311A PRO* 1.3 84.1 - - + +
313A ALA* 1.3 58.3 + - - +
315A ALA* 4.1 7.2 - - - +
316A LEU* 2.9 30.5 + - - +
337A HIS* 3.4 21.7 + - - -
338A SER* 3.5 28.1 + - - +
339A PHE* 3.8 24.5 - - + +
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Residues in contact with ALA 313 (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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247A LEU* 4.1 3.8 - - + +
251A LEU* 3.8 29.2 - - + -
309A THR* 4.4 2.9 - - + -
310A PRO* 2.9 16.8 + - + +
312A GLU* 1.3 80.1 - - - +
314A ILE* 1.3 60.5 + - - +
316A LEU* 3.5 3.1 + - - +
317A CYS* 3.0 24.8 + - - +
339A PHE* 3.4 36.5 - - + -
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Residues in contact with ILE 314 (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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301A TRP* 3.6 34.7 - - + +
302A THR* 4.1 33.7 - - + +
305A PHE* 3.7 25.1 - - + -
306A ARG 5.5 0.7 - - - +
309A THR* 3.8 33.9 - - + +
310A PRO 3.3 3.3 + - - +
311A PRO* 3.2 12.0 + - + +
313A ALA* 1.3 75.0 - - - +
315A ALA* 1.3 63.9 + - - +
317A CYS* 3.1 9.1 + - - +
318A SER* 3.0 22.1 + - - -
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Residues in contact with ALA 315 (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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311A PRO 2.9 17.1 + - - +
312A GLU* 3.7 16.8 - - - +
314A ILE* 1.3 74.6 - - - +
316A LEU* 1.3 63.5 + - - +
318A SER* 2.8 24.4 + - - -
319A ARG* 3.3 13.8 - - + +
337A HIS* 4.2 8.5 - - + +
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Residues in contact with LEU 316 (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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166A PHE* 4.6 4.5 - - + -
247A LEU* 3.7 19.7 - - + -
312A GLU 2.9 18.3 + - - +
313A ALA 3.7 4.0 - - - +
315A ALA* 1.3 75.3 - - - +
317A CYS* 1.3 64.1 + - - +
319A ARG* 3.0 12.2 + - - +
320A LEU* 3.3 30.8 + - + +
329A LEU* 3.8 25.1 - - + -
334A ALA* 4.5 6.7 - - + -
337A HIS* 3.6 25.7 + - + +
339A PHE* 3.7 29.4 - - + -
340A PHE* 3.8 20.9 - - + -
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Residues in contact with CYS 317 (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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244A GLY 4.3 4.9 - - - -
247A LEU* 3.7 26.5 - - - -
248A ALA* 3.9 19.7 - - - -
251A LEU* 4.4 1.3 - - - -
301A TRP* 4.4 15.5 - - + -
305A PHE* 3.9 23.1 - - + -
313A ALA 3.0 11.6 + - - +
314A ILE* 3.1 13.2 + - - +
316A LEU* 1.3 76.6 - - - +
318A SER* 1.3 62.7 + - - +
319A ARG 3.0 0.2 - - - -
320A LEU* 3.0 6.5 + - - +
321A LEU* 3.0 30.2 + - - +
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Residues in contact with SER 318 (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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301A TRP* 3.5 40.7 + - - +
314A ILE 3.0 10.3 + - - -
315A ALA* 2.8 22.9 + - - -
317A CYS* 1.3 76.6 - - - +
319A ARG* 1.3 63.5 + - - +
321A LEU 4.0 5.6 - - - +
322A GLU* 3.2 25.8 - - - +
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Residues in contact with ARG 319 (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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315A ALA* 3.3 15.7 - - + +
316A LEU* 3.0 9.9 + - - +
318A SER* 1.3 81.9 - - - +
320A LEU* 1.3 60.3 + - - +
322A GLU* 2.8 35.3 + - - -
327A ALA* 3.1 25.9 + - - +
328A ARG* 3.5 6.6 - - - -
329A LEU* 3.1 63.4 + - + +
337A HIS* 5.1 6.1 - - + -
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Residues in contact with LEU 320 (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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166A PHE* 3.6 33.7 - - + -
240A VAL* 3.4 29.3 - - + +
241A TRP* 4.2 6.9 - - - -
243A ALA 4.7 0.2 - - - -
244A GLY* 3.6 28.0 - - - +
247A LEU* 4.1 9.9 - - + -
316A LEU* 3.3 33.2 - - + +
317A CYS* 3.0 5.9 + - - +
319A ARG* 1.3 79.4 - - - +
321A LEU* 1.3 62.6 + - - +
322A GLU 3.0 7.9 + - - -
328A ARG* 3.2 22.6 + - - +
329A LEU* 4.2 19.3 - - + -
334A ALA* 4.4 1.6 - - + -
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Residues in contact with LEU 321 (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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241A TRP* 3.5 60.6 - - + +
244A GLY* 3.9 20.9 - - - +
245A CYS* 3.9 11.7 - - - +
248A ALA* 4.5 10.3 - - + -
256A ILE* 4.7 0.9 - - + -
257A PHE* 4.1 13.9 - - + -
273A LEU* 3.4 23.5 - - + +
301A TRP* 3.5 33.0 - - + -
317A CYS* 3.0 14.0 + - - +
318A SER 4.0 7.1 - - - +
320A LEU* 1.3 72.7 - - - +
322A GLU* 1.3 60.4 + - - +
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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