Contacts of the helix formed by residues 311 - 327 (chain A) in PDB entry 2IBI
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 HIS 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A ASN* 4.2 2.0 - - - +
310A ALA* 1.3 100.9 + - + +
312A THR* 1.3 65.3 + - - +
313A ALA 3.0 3.4 - - - +
314A LEU* 3.1 22.3 + - + +
315A VAL 4.0 0.9 + - - -
342A GLN* 5.0 3.7 + - - -
345A ARG* 3.9 16.6 - - + +
346A TYR* 3.6 57.6 + + + +
372A GLU* 3.4 37.5 + - + +
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.0 26.1 - - + +
305A HIS 5.1 3.1 - - - +
307A GLY 4.7 0.2 + - - -
309A ASN* 2.9 41.8 + - - +
310A ALA 3.7 1.2 - - - -
311A HIS* 1.3 77.7 - - - +
313A ALA* 1.3 61.9 + - - +
314A LEU 3.4 0.9 + - - -
315A VAL* 3.5 5.9 + - - +
316A GLU* 3.5 36.1 + - - +
372A GLU* 3.6 10.0 + - - -
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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
----------------------------------------------------------
310A ALA 4.8 3.6 + - - +
311A HIS* 3.0 1.4 - - - +
312A THR* 1.3 77.6 - - - +
314A LEU* 1.3 53.7 + - - +
316A GLU* 4.0 11.4 + - - +
317A GLU* 2.8 43.5 + - + +
342A GLN* 2.9 32.8 - - + +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A HIS* 3.1 19.8 + - + +
313A ALA* 1.3 78.0 - - - +
315A VAL* 1.3 57.5 + - + +
317A GLU* 3.9 1.0 - - - +
318A PHE* 2.9 31.4 + - - +
339A PHE* 4.1 13.9 - - + -
342A GLN* 3.9 15.2 + - + +
343A ILE* 3.8 51.8 - - + +
346A TYR* 4.2 14.1 - - + -
365A LEU* 4.2 4.0 - - + +
368A GLY* 3.7 37.5 - - - +
369A LEU* 4.0 8.3 - - + +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 5.6 2.0 - - + -
300A TYR* 3.9 30.7 - - + -
304A LEU* 4.0 18.8 - - + -
311A HIS 4.0 0.2 + - - -
312A THR 3.5 4.4 + - - +
314A LEU* 1.3 76.3 - - + +
316A GLU* 1.3 58.7 + - - +
318A PHE* 3.9 2.7 - - + +
319A ALA* 3.0 28.1 + - + +
368A GLY 4.6 0.2 - - - +
369A LEU* 3.7 37.9 - - + +
372A GLU* 3.6 30.7 - - + -
373A VAL* 4.1 7.9 - - + -
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 4.5 13.3 + - + -
301A MET* 6.1 0.7 - - - +
304A LEU* 3.9 23.1 - - + +
312A THR* 3.5 34.5 + - - +
313A ALA* 3.9 8.3 - - - +
314A LEU 3.3 0.2 - - - -
315A VAL* 1.3 78.3 - - - +
317A GLU* 1.3 60.0 + - + +
319A ALA* 3.5 5.6 + - - +
320A LYS* 3.0 29.5 + - - +
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Residues in contact with GLU 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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313A ALA* 2.8 31.6 + - + +
314A LEU 4.1 2.0 - - - +
316A GLU* 1.3 72.6 - - + +
318A PHE* 1.3 64.6 + - - +
320A LYS* 3.4 15.5 + - - +
321A LEU* 3.1 25.5 + - - +
338A GLU* 3.3 34.4 - - + +
339A PHE* 4.1 21.9 + - - +
342A GLN* 3.7 19.7 - - + +
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Residues in contact with PHE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.2 14.6 - - + -
285A LEU* 4.1 22.4 - - + -
291A LEU* 4.0 29.6 - - + -
295A CYS* 3.6 26.9 - - - -
314A LEU 2.9 19.0 + - - +
315A VAL* 3.9 3.6 - - + +
317A GLU* 1.3 75.4 - - - +
319A ALA* 1.3 66.4 + - - +
320A LYS 3.2 0.2 + - - -
321A LEU* 3.3 7.1 + - + +
322A ILE* 3.1 44.0 + - + +
339A PHE* 3.8 28.1 - + + -
365A LEU* 4.5 0.9 - - + -
369A LEU* 3.8 35.4 - - + -
411A ILE* 6.3 0.2 - - + -
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A CYS* 3.9 19.3 - - - +
300A TYR* 3.5 41.3 - - + +
315A VAL* 3.0 20.9 + - + +
316A GLU 3.7 3.1 - - - +
318A PHE* 1.3 77.8 - - + +
320A LYS* 1.3 57.6 + - - +
322A ILE* 3.5 2.8 + - - +
323A GLN* 3.0 35.3 + - - +
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Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 5.2 0.4 + - - +
316A GLU 3.0 19.3 + - - +
317A GLU* 3.9 16.4 - - - +
318A PHE 3.2 0.4 - - - -
319A ALA* 1.3 74.5 - - - +
321A LEU* 1.3 53.5 + - - +
323A GLN* 3.4 16.1 + - + +
324A THR* 2.8 49.6 + - - +
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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
----------------------------------------------------------
269A LEU* 4.1 10.8 - - + -
282A LEU* 3.8 32.1 - - + -
317A GLU 3.1 12.7 + - - +
318A PHE 3.3 9.9 - - - +
320A LYS* 1.3 73.4 - - - +
322A ILE* 1.3 62.5 + - + +
324A THR* 3.3 5.3 + - - -
325A ILE* 2.9 38.3 + - + +
334A VAL* 3.4 31.0 - - + -
335A SER 4.7 1.6 - - - +
336A PRO* 3.7 33.9 - - + -
339A PHE* 4.0 15.5 - - + -
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Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.2 6.7 - - + +
285A LEU 4.4 0.9 - - - +
286A SER* 3.5 35.7 - - - +
292A ARG* 4.1 30.7 - - + +
295A CYS* 3.9 19.3 - - + -
296A LEU* 4.2 2.7 - - + -
318A PHE* 3.1 46.5 + - + +
319A ALA 3.8 6.3 - - - +
321A LEU* 1.3 79.7 - - + +
323A GLN* 1.3 58.2 + - - +
325A ILE* 3.3 10.2 + - + +
326A TRP* 3.0 34.0 + - + +
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Residues in contact with GLN 323 (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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295A CYS 2.7 28.3 + - - +
296A LEU* 3.7 20.6 - - + +
298A ARG* 4.3 15.6 + - - +
300A TYR* 3.0 26.4 + - - -
319A ALA 3.0 22.7 + - - +
320A LYS* 3.5 18.6 - - + +
322A ILE* 1.3 76.3 - - - +
324A THR* 1.3 62.6 + - - +
326A TRP 3.3 1.2 + - - -
327A THR* 3.1 32.4 + - + +
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Residues in contact with THR 324 (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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320A LYS* 2.8 37.8 + - - +
321A LEU* 3.3 8.2 + - - -
323A GLN* 1.3 69.1 - - - +
325A ILE* 1.3 66.2 + - - +
327A THR* 3.3 7.3 + - - -
328A SER* 3.2 25.2 + - - -
334A VAL* 3.6 29.8 - - + -
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Residues in contact with ILE 325 (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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265A GLY* 3.6 29.4 + - - +
267A ALA* 4.0 18.5 - - + +
269A LEU* 4.2 31.0 - - + -
282A LEU* 5.0 3.4 - - + +
283A GLN* 4.4 9.9 - - - +
286A SER* 3.7 33.4 - - - +
321A LEU* 2.9 30.1 + - + +
322A ILE* 3.3 10.3 + - + +
324A THR* 1.3 74.7 - - - +
326A TRP* 1.3 64.6 + - + +
328A SER* 2.9 20.3 + - - -
334A VAL* 4.5 8.7 - - + -
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Residues in contact with TRP 326 (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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264A GLN* 3.3 59.5 - - + +
265A GLY* 3.5 20.6 - - - -
286A SER* 2.9 34.8 + - - -
287A ASN* 3.6 20.9 - - - -
292A ARG* 3.4 51.8 - - + +
296A LEU* 4.0 22.8 - - + +
322A ILE* 3.0 26.0 + - + +
323A GLN 3.3 0.4 + - - +
324A THR 3.2 0.2 - - - -
325A ILE* 1.3 79.0 - - + +
327A THR* 1.3 63.7 + - - +
328A SER 3.6 0.4 - - - -
564A SER* 3.8 9.0 - - - -
565A PRO* 3.7 15.7 - - + -
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Residues in contact with THR 327 (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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264A GLN* 5.4 2.2 - - - +
296A LEU* 5.8 2.9 - - + -
323A GLN* 3.1 21.8 + - + +
324A THR* 3.6 8.8 + - - +
325A ILE 3.3 0.2 - - - -
326A TRP* 1.3 80.9 - - + +
328A SER* 1.3 61.4 + - - +
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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