Contacts of the helix formed by residues 340 - 361 (chain A) in PDB entry 4IKV
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 340 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA 4.3 2.0 - - - -
170A PHE* 2.7 38.9 + - - -
173A PRO* 3.4 17.3 - - - +
174A LEU* 3.5 14.4 - - - +
337A TRP 2.9 13.3 + - - -
339A GLN* 1.3 78.7 - - - +
341A LEU* 1.3 64.2 + - - +
342A ASN 3.5 0.4 - - - -
343A PRO* 3.3 9.2 - - - +
344A LEU* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A TRP 4.8 1.3 - - - +
338A PHE* 3.1 46.0 + - + +
340A SER* 1.3 77.4 - - - +
342A ASN* 1.3 67.8 + - - +
344A LEU* 3.3 14.5 + - + -
345A PHE* 2.9 57.8 + - + -
403A VAL* 4.0 25.8 - - + -
406A TYR* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 5.1 1.2 - - - +
309A GLN* 3.4 20.3 + - - +
338A PHE 4.5 1.4 + - - -
339A GLN 4.4 3.1 + - - +
341A LEU* 1.3 78.6 - - - +
343A PRO* 1.3 72.2 - - + +
345A PHE* 5.0 0.2 - - - -
346A ILE* 3.1 41.6 + - - +
406A TYR* 4.8 15.7 + - + +
409A VAL* 4.8 4.0 - - - +
410A VAL* 3.6 21.4 - - - +
413A GLU* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 3.5 41.2 - - - +
169A ALA* 3.6 35.2 - - + +
170A PHE* 3.7 3.1 - - + +
339A GLN 3.4 13.0 - - - +
340A SER 3.3 14.4 - - - +
342A ASN* 1.3 95.2 - - + +
344A LEU* 1.3 63.3 + - - +
346A ILE* 3.2 2.0 + - + +
347A ILE* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PHE* 3.9 30.8 - - + -
340A SER 3.1 20.5 + - - +
341A LEU* 3.6 16.8 - - + +
343A PRO* 1.3 74.9 - - - +
345A PHE* 1.3 82.0 + - + +
347A ILE* 3.2 10.0 + - + +
348A ILE* 3.0 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 2.9 51.7 + - + +
344A LEU* 1.3 94.4 - - + +
346A ILE* 1.3 58.3 + - - +
348A ILE* 4.5 11.4 - - + -
349A LEU* 2.8 42.1 + - + +
403A VAL* 4.0 20.6 - - + -
406A TYR 4.2 3.6 - - - -
407A PHE* 3.7 53.4 - + + -
410A VAL* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 3.3 30.1 - - - +
342A ASN* 3.1 41.0 + - - +
343A PRO 3.7 4.0 - - - +
345A PHE* 1.3 78.6 - - - +
347A ILE* 1.3 57.3 + - - +
350A ALA* 2.9 40.8 + - + +
410A VAL* 3.9 19.7 - - + -
413A GLU* 3.7 26.5 - - + +
414A LEU* 4.6 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A MET* 5.8 5.4 - - + +
166A ASN* 3.9 39.5 - - + +
167A LEU* 4.5 13.9 - - + +
170A PHE* 4.6 9.9 - - + -
343A PRO 3.0 22.4 + - - +
344A LEU* 3.6 9.2 - - + +
346A ILE* 1.3 79.1 - - - +
348A ILE* 1.3 65.2 + - + +
350A ALA* 4.7 1.0 - - - +
351A PRO* 3.5 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.0 47.6 + - + +
345A PHE* 4.0 13.2 - - + +
347A ILE* 1.3 81.5 - - + +
349A LEU* 1.3 74.4 + - + +
351A PRO* 3.5 9.9 - - - +
352A VAL* 3.9 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 2.8 28.6 + - + +
348A ILE* 1.3 88.3 - - + +
350A ALA* 1.3 64.6 + - - +
351A PRO 3.4 0.9 - - - -
352A VAL* 2.9 27.6 + - + +
353A PHE* 3.0 20.9 + - + -
407A PHE* 3.5 37.5 - - + -
410A VAL* 4.2 13.0 - - + -
411A LEU* 4.0 19.3 - - + -
414A LEU* 3.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 2.9 28.8 + - + +
347A ILE* 4.7 1.6 - - - +
349A LEU* 1.3 71.9 - - - +
351A PRO* 1.3 68.6 - - + +
353A PHE* 3.3 3.6 + - - +
354A ALA* 3.0 22.6 + - - +
414A LEU* 3.7 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ILE 3.5 20.6 - - - +
348A ILE 3.5 6.5 - - - +
349A LEU 3.5 3.8 - - - -
350A ALA* 1.3 92.3 - - + +
352A VAL* 1.3 57.9 + - + +
354A ALA* 3.4 8.2 + - + +
355A TRP* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 3.9 17.7 - - + +
349A LEU* 2.9 20.0 + - + +
351A PRO* 1.3 76.9 - - + +
353A PHE* 1.3 65.3 + - + +
355A TRP* 3.3 15.5 + - + +
356A MET* 2.9 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.0 26.2 + - + +
350A ALA* 3.7 7.9 - - - +
352A VAL* 1.3 82.1 - - + +
354A ALA* 1.3 63.4 + - - +
356A MET* 3.0 31.1 + - + +
357A TRP* 2.9 46.3 + + - +
411A LEU* 3.7 52.3 - - + -
414A LEU* 3.7 35.0 - - + +
415A CYS* 4.1 13.0 - - - -
609A OLA 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA 3.0 17.0 + - - +
351A PRO* 3.7 8.5 - - + +
353A PHE* 1.3 77.1 - - - +
355A TRP* 1.3 62.1 + - - +
357A TRP* 3.5 11.2 + - - +
358A VAL* 3.3 27.0 + - - +
613A PG4 5.4 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A PRO 3.0 18.2 + - - +
352A VAL* 3.5 16.4 - - + +
354A ALA* 1.3 76.9 - - - +
356A MET* 1.3 83.8 + - + +
358A VAL* 3.1 11.3 + - + +
359A LYS* 2.9 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 2.9 14.1 + - + +
353A PHE* 3.3 41.7 - - + +
355A TRP* 1.3 91.7 - - + +
357A TRP* 1.3 70.5 + - + +
359A LYS* 3.2 4.5 + - - +
360A LEU* 2.9 44.4 + - + +
609A OLA 3.8 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PHE* 2.9 54.4 + + - +
354A ALA* 3.9 9.4 - - - +
355A TRP 3.3 0.2 - - - -
356A MET* 1.3 91.6 - - + +
358A VAL* 1.3 62.4 + - - +
360A LEU* 3.4 17.6 + - + +
361A GLY* 3.0 20.3 + - - -
364A GLN* 3.5 26.1 - - - +
365A PRO* 3.6 26.5 - - + -
370A LYS* 3.8 29.3 - - + +
373A LEU* 5.2 0.7 - - + -
414A LEU 4.2 13.9 + - - -
415A CYS* 4.4 16.6 - - - -
418A PRO* 6.0 2.6 - - - +
609A OLA 4.2 12.1 - - + -
613A PG4 3.6 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ALA 3.3 15.0 + - - +
355A TRP* 3.1 12.7 + - + +
357A TRP* 1.3 78.2 - - - +
359A LYS* 1.3 77.8 + - + +
361A GLY* 3.2 14.3 + - - -
613A PG4 4.3 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TRP* 2.9 67.0 + - + +
356A MET* 3.2 6.3 + - - +
358A VAL* 1.3 88.0 - - - +
360A LEU* 1.3 62.9 + - + +
363A ARG* 3.1 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A MET* 2.9 38.8 + - + +
357A TRP* 3.8 17.9 - - + +
359A LYS* 1.3 77.7 - - + +
361A GLY* 1.3 65.9 + - - +
363A ARG* 2.9 44.6 + - + +
364A GLN* 3.8 18.4 - - + -
609A OLA 3.9 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TRP 3.0 13.1 + - - -
358A VAL 3.2 12.4 + - - -
360A LEU* 1.3 73.8 - - - +
362A LYS* 1.3 62.3 + - - -
363A ARG* 4.5 4.5 - - - -
364A GLN* 3.1 29.3 + - - +
613A PG4 5.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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