Contacts of the helix formed by residues 305 - 323 (chain A) in PDB entry 4I2C
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 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASN* 1.4 68.7 - - - +
306A PRO* 1.4 74.1 - - + +
308A ALA* 3.1 7.5 + - - +
309A GLU* 2.9 31.9 + - + +
334A PHE* 4.0 9.4 - - + -
337A GLY 4.3 11.2 + - - -
338A LYS 3.8 16.8 - - - +
339A MET* 3.5 54.5 + - - +
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Residues in contact with PRO 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASN* 3.2 16.8 - - + +
305A ARG* 1.4 91.5 - - + +
307A GLU* 1.4 54.3 - - - +
309A GLU* 3.5 7.7 + - + +
310A ALA* 3.0 27.4 + - - +
415A VAL* 3.8 12.8 - - + +
416A HIS 3.7 23.3 + - - +
417A SER* 3.8 26.2 - - - -
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A CYS 3.7 0.2 - - - +
303A VAL* 3.5 11.9 - - + +
304A ASN* 3.0 43.7 + - - +
306A PRO* 1.4 73.5 - - - +
308A ALA* 1.4 59.2 + - - +
310A ALA* 3.2 3.9 + - - +
311A VAL* 3.0 34.6 + - - +
410A LEU* 3.9 23.7 - - + +
412A HIS* 6.1 1.2 - - - -
415A VAL* 4.1 17.0 - - + +
429A LYS* 3.0 44.6 + - + +
431A ILE* 4.5 1.1 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 4.0 0.6 - - - +
304A ASN 2.9 14.6 + - - +
305A ARG* 3.1 7.6 + - - +
307A GLU* 1.4 75.0 - - - +
309A GLU* 1.3 56.5 + - + +
311A VAL* 3.3 3.8 + - - +
312A SER 2.9 23.2 + - - -
330A MET* 3.3 26.3 - - + +
334A PHE* 3.9 31.2 - - + -
344A VAL* 3.9 17.6 - - + +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG* 2.9 23.1 + - + +
306A PRO* 3.7 7.4 - - + +
308A ALA* 1.3 75.0 - - + +
310A ALA* 1.3 64.2 + - - +
312A SER* 3.2 14.4 + - - -
313A MET* 3.1 27.7 + - + +
316A LYS* 5.9 0.7 + - - -
330A MET* 4.2 15.2 - - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO 3.0 15.4 + - - +
307A GLU 3.2 7.6 + - - +
309A GLU* 1.3 75.0 - - - +
311A VAL* 1.4 61.5 + - - +
313A MET* 3.4 11.1 + - - +
314A LEU* 3.2 23.9 + - - +
410A LEU* 3.8 20.8 - - + +
414A ARG* 3.5 31.2 + - + +
415A VAL* 4.0 6.3 - - + -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU 3.0 18.8 + - - +
308A ALA* 3.6 9.0 - - - +
310A ALA* 1.4 73.8 - - - +
312A SER* 1.4 57.7 + - - +
314A LEU* 3.0 11.9 + - + +
315A VAL* 2.9 32.3 + - + +
344A VAL* 4.4 4.9 - - + -
346A PHE* 3.7 19.3 - - + -
408A LEU* 4.9 7.9 - - + -
410A LEU* 4.1 17.3 - - + -
431A ILE* 3.9 27.4 - - + -
433A VAL* 3.6 26.2 - - + -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA 2.9 13.2 + - - -
309A GLU* 3.2 17.1 + - - -
311A VAL* 1.4 73.2 - - - +
313A MET* 1.3 58.3 + - - +
315A VAL* 3.4 1.9 + - - +
316A LYS* 2.9 57.9 + - - +
330A MET* 3.8 12.9 + - - +
346A PHE* 3.5 28.0 - - - -
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLU* 3.1 15.0 + - + +
310A ALA* 3.5 11.7 - - - +
312A SER* 1.3 76.0 - - - +
314A LEU* 1.4 58.4 + - - +
316A LYS* 3.9 13.7 - - + +
317A GLU* 2.9 59.3 + - + +
414A ARG* 4.9 6.3 - - - +
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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
----------------------------------------------------------
310A ALA 3.2 5.8 + - - +
311A VAL* 3.0 13.5 + - + +
313A MET* 1.4 75.2 - - - +
315A VAL* 1.4 65.0 + - + +
317A GLU* 3.5 8.5 + - + +
318A ALA* 3.1 25.1 + - - +
369A TRP* 3.8 16.8 + - + +
374A LEU* 4.3 22.9 - - + -
408A LEU* 5.1 14.1 - - + -
409A LYS 4.7 11.9 - - - +
410A LEU* 4.0 27.6 - - + -
414A ARG* 3.5 39.0 - - - +
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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
----------------------------------------------------------
311A VAL* 2.9 26.6 + - + +
312A SER* 3.7 6.5 - - - +
314A LEU* 1.4 75.2 - - + +
316A LYS* 1.3 56.6 + - - +
318A ALA* 3.3 2.8 + - - +
319A VAL* 2.9 44.9 + - + +
328A VAL* 3.7 23.3 - - + -
346A PHE* 3.8 25.8 - - + -
348A ILE* 4.6 2.0 - - + -
369A TRP* 3.9 20.0 - - + -
408A LEU* 5.3 0.4 - - + -
433A VAL* 4.5 2.0 - - + -
435A LEU* 3.9 26.5 - - + -
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Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLU* 5.9 0.8 + - - -
312A SER* 2.9 38.7 + - - +
313A MET* 3.9 14.4 - - + +
315A VAL* 1.3 73.8 - - - +
317A GLU* 1.4 55.9 - - + +
319A VAL* 3.4 0.3 + - - +
320A VAL* 3.0 42.5 + - + +
328A VAL* 3.8 47.9 + - + -
330A MET 6.2 0.4 - - - +
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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
----------------------------------------------------------
313A MET* 2.9 39.5 + - + +
314A LEU* 3.7 8.8 - - - +
316A LYS* 1.4 75.4 - - - +
318A ALA* 1.3 53.4 + - - +
320A VAL* 3.9 8.1 - - - +
321A THR* 2.6 31.5 + - - -
368A PHE* 5.4 3.1 - - + -
414A ARG* 3.1 27.7 + - - -
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Residues in contact with ALA 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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314A LEU 3.1 17.9 + - - +
315A VAL 3.7 3.1 - - - +
317A GLU* 1.3 74.2 - - - +
319A VAL* 1.3 63.9 + - - +
321A THR* 3.2 11.5 - - - -
322A PHE* 3.2 22.7 - - - -
365A VAL* 3.8 14.8 - - + -
368A PHE* 4.0 19.9 - - + -
369A TRP* 3.7 29.2 - - + +
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 2.9 29.1 + - + +
316A LYS 3.4 2.7 + - - +
318A ALA* 1.3 75.1 - - - +
320A VAL* 1.4 59.0 + - + +
322A PHE* 3.1 4.9 + - - -
323A LEU 2.9 23.9 + - - -
326A ALA* 3.5 29.8 - - + -
328A VAL* 3.8 15.9 - - + -
348A ILE* 3.9 34.1 - - + -
361A LEU* 3.9 11.8 - - + +
365A VAL* 3.9 21.5 - - + -
435A LEU* 5.8 0.2 - - + -
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LYS* 3.0 30.2 + - + +
317A GLU* 3.9 9.9 - - - +
319A VAL* 1.4 74.7 - - + +
321A THR* 1.3 65.4 + - - +
323A LEU 3.4 10.5 - - - +
324A PRO* 3.4 41.8 - - + +
326A ALA 4.6 11.0 - - - +
328A VAL* 5.8 1.6 - - + -
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Residues in contact with THR 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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317A GLU 2.6 22.2 + - - -
318A ALA* 3.2 14.7 - - - -
319A VAL 3.2 0.2 - - - -
320A VAL* 1.3 80.8 - - - +
322A PHE* 1.4 76.6 + - + +
324A PRO* 5.3 1.0 - - - +
368A PHE* 5.3 14.5 - - + -
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Residues in contact with PHE 322 (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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318A ALA 3.2 26.7 - - - -
319A VAL 3.1 2.0 + - - -
321A THR* 1.4 97.1 - - + +
323A LEU* 1.4 64.6 + - - +
324A PRO* 3.9 7.0 - - - +
357A GLU* 5.3 2.1 - - - +
361A LEU* 3.8 14.1 - - + -
364A LYS* 3.6 63.9 + - + +
365A VAL* 3.8 17.7 - - + -
368A PHE* 3.9 20.4 - + + -
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A VAL 2.9 8.3 + - - +
320A VAL* 3.4 12.4 - - - +
322A PHE* 1.4 81.5 - - - +
324A PRO* 1.4 67.7 - - + +
325A ASP* 3.2 8.3 - - - +
326A ALA* 3.1 24.9 + - + +
350A SER* 3.9 23.1 - - - +
353A ALA* 3.8 26.0 - - + +
357A GLU* 4.4 26.2 - - + +
361A LEU* 3.9 34.3 - - + -
437A MET* 4.2 8.3 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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