Contacts of the helix formed by residues 302 - 317 (chain A) in PDB entry 2IVF
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A VAL* 3.7 2.1 - - - +
299A ARG* 2.6 40.7 + - - -
300A VAL 3.3 0.6 - - - -
301A GLY* 1.3 76.1 - - - +
303A ASP* 1.3 64.8 + - - +
304A ALA 3.2 3.1 - - - -
305A ALA* 3.0 19.6 + - - +
420A LYS 3.7 9.6 - - - -
421A CYS* 3.2 29.8 - - - +
831A HIS* 3.5 16.2 - - - -
833A ASP* 4.4 3.1 - - - -
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.4 10.9 + - - -
254A CYS* 4.3 0.7 - - - -
281A ILE* 3.6 7.8 - - + +
298A VAL* 3.6 14.3 - - - +
301A GLY 3.4 2.4 + - - -
302A SER* 1.3 74.5 + - - +
304A ALA* 1.3 63.8 + - - +
306A PHE* 3.0 10.5 + - - +
307A TRP* 3.0 38.7 + - + +
457A MET* 3.5 28.7 - - + +
1986A MGD 2.6 50.9 + - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A SER 3.1 0.8 + - - -
303A ASP* 1.3 76.5 - - - +
305A ALA* 1.3 57.6 + - - +
307A TRP 3.2 0.9 + - - -
308A LEU* 2.7 36.4 + - - +
456A LEU* 4.0 8.1 - - + +
457A MET* 4.0 14.8 - - + +
460A SER* 3.5 22.3 - - - +
830A THR 3.4 26.2 - - - +
831A HIS* 3.8 12.6 - - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A SER 3.0 12.0 + - - +
304A ALA* 1.3 79.1 - - - +
306A PHE* 1.3 62.8 + - - +
308A LEU* 4.0 0.3 - - - +
309A GLY 2.9 17.3 + - - -
412A TYR* 4.0 16.8 - - + -
417A ALA* 3.3 21.7 - - - +
420A LYS* 3.7 30.3 - - + -
421A CYS* 4.1 3.8 - - + -
831A HIS* 3.9 15.9 - - + +
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Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 4.6 1.1 - + - -
281A ILE* 3.7 24.7 - - + -
296A VAL* 3.7 27.1 - - + -
298A VAL* 4.2 11.7 - - + -
302A SER 3.6 2.2 + - - -
303A ASP* 3.0 8.6 + - - +
305A ALA* 1.3 78.5 - - - +
307A TRP* 1.3 78.3 + + - +
309A GLY* 3.1 4.0 + - - -
310A LEU* 3.0 67.9 + - + +
417A ALA* 5.1 0.9 - - - -
421A CYS* 3.9 17.6 - - - -
423A VAL* 4.1 17.3 - - + -
428A ILE* 4.2 12.2 - - + +
431A LEU* 3.8 25.4 - - + -
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Residues in contact with TRP 307 (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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251A PHE* 3.7 35.0 - + + -
253A THR* 5.0 1.4 + - - -
281A ILE* 3.4 26.0 - - + +
303A ASP* 3.0 37.8 + - + +
306A PHE* 1.3 85.0 - + - +
308A LEU* 1.3 62.3 + - - +
310A LEU* 3.3 29.8 + - + +
311A SER* 3.0 30.5 + - - -
435A VAL* 4.6 1.3 - - + -
457A MET 4.1 5.6 - - - -
460A SER* 3.5 24.7 - - - +
461A LEU* 3.5 41.6 - - + +
464A ALA* 3.6 24.2 - - + +
465A MET* 3.7 23.3 - - + -
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Residues in contact with LEU 308 (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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304A ALA 2.7 24.3 + - - +
307A TRP* 1.3 72.8 - - - +
309A GLY* 1.3 58.7 + - - +
311A SER* 3.2 1.7 + - - -
312A GLN* 2.8 30.7 + - - +
405A LEU* 5.2 0.2 - - + -
408A HIS* 4.5 2.2 - - + +
409A LEU* 3.5 20.0 - - + +
412A TYR* 3.7 42.2 - - + -
460A SER* 3.7 16.8 - - - +
463A LEU* 4.0 22.0 - - + -
829A PRO* 3.8 13.2 - - + +
830A THR* 3.5 35.4 - - - +
831A HIS 3.8 0.2 - - - +
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Residues in contact with GLY 309 (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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305A ALA 2.9 15.2 + - - -
306A PHE 3.1 5.3 + - - -
308A LEU* 1.3 76.5 - - - +
310A LEU* 1.3 54.8 + - - +
312A GLN* 3.2 3.3 + - - +
313A VAL* 2.9 32.9 + - - +
412A TYR* 3.4 18.0 + - - +
413A THR 5.0 0.4 - - - -
414A PRO* 4.8 0.3 - - - +
417A ALA* 3.9 10.1 - - - -
428A ILE* 3.9 12.3 - - - +
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Residues in contact with LEU 310 (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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251A PHE* 4.6 0.9 - - + -
306A PHE* 3.0 49.0 + - + +
307A TRP* 3.5 43.1 - - + +
308A LEU 3.2 0.2 - - - -
309A GLY* 1.3 76.2 - - - +
311A SER* 1.3 61.2 + - - +
313A VAL* 3.3 4.8 + - - +
314A MET* 3.1 30.5 + - + +
428A ILE* 3.3 26.0 - - + +
431A LEU* 4.1 5.2 - - + +
432A GLY* 3.6 19.1 - - - +
435A VAL* 3.8 19.5 - - + -
464A ALA* 4.6 4.7 - - + -
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TRP 3.0 14.8 + - - -
308A LEU* 3.2 8.9 + - - -
310A LEU* 1.3 74.3 - - - +
312A GLN* 1.3 61.1 + - - +
314A MET* 3.3 5.7 + - - +
315A ILE* 2.9 34.3 + - - +
409A LEU* 4.1 11.9 - - - -
460A SER 4.3 0.2 + - - -
463A LEU* 3.8 13.2 - - - +
464A ALA* 3.6 17.5 + - - -
467A LEU* 3.4 28.3 - - - +
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Residues in contact with GLN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU 2.8 12.0 + - - +
309A GLY 3.5 1.3 - - - +
311A SER* 1.3 76.2 - - - +
313A VAL* 1.3 64.2 + - - +
315A ILE* 4.0 1.3 - - - +
316A ASP* 2.8 58.8 + - - +
409A LEU* 3.3 40.6 - - + +
410A LYS* 5.7 0.3 - - - -
412A TYR 3.3 17.9 - - - +
413A THR* 3.8 18.5 - - - +
414A PRO* 3.3 25.5 - - - +
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Residues in contact with VAL 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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309A GLY 2.9 20.7 + - - +
310A LEU 3.5 8.3 - - - +
311A SER 3.2 0.4 - - - -
312A GLN* 1.3 78.7 - - - +
314A MET* 1.3 57.2 + - - +
316A ASP* 4.7 1.3 - - - -
317A GLU* 2.9 58.9 + - - +
319A LEU* 4.7 1.1 - - + -
414A PRO* 3.7 27.6 - - + -
428A ILE* 4.3 3.6 - - + +
429A ARG* 4.1 27.1 - - + +
432A GLY* 4.0 22.4 - - - -
433A ARG* 4.1 2.5 - - + +
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Residues in contact with MET 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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310A LEU* 3.1 17.3 + - + +
311A SER* 3.8 7.4 - - - +
313A VAL* 1.3 76.5 - - - +
315A ILE* 1.3 61.4 + - - +
318A LYS* 3.2 1.6 + - - -
319A LEU* 2.8 39.1 + - + -
320A PHE* 3.5 14.1 + - + +
432A GLY 3.4 19.7 - - - +
435A VAL* 4.2 7.2 - - + -
436A ALA* 3.7 28.0 - - + -
464A ALA* 3.3 44.0 - - + +
467A LEU* 3.9 15.0 - - + -
468A SER* 3.9 16.4 - - - -
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Residues in contact with ILE 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 SER 2.9 15.8 + - - +
312A GLN* 4.0 3.6 - - - +
314A MET* 1.3 76.4 - - - +
316A ASP* 1.3 68.6 + - - +
318A LYS* 2.9 18.7 + - - +
320A PHE* 3.8 9.5 - - + -
402A PHE* 3.8 41.1 - - + -
405A LEU* 4.1 9.6 - - + -
406A ARG* 4.2 24.0 - - + +
409A LEU* 3.6 27.4 - - + -
467A LEU* 3.9 24.2 - - + -
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Residues in contact with ASP 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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312A GLN* 2.8 45.4 + - - +
313A VAL* 4.0 2.5 - - - +
315A ILE* 1.3 76.0 - - - +
317A GLU* 1.3 64.3 + - + +
318A LYS* 3.6 8.3 + - - +
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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 VAL* 2.9 27.8 + - + +
316A ASP* 1.3 81.6 - - + +
318A LYS* 1.3 71.6 + - - +
319A LEU* 3.3 23.4 + - + +
429A ARG* 4.0 13.0 + - - +
433A ARG* 2.7 55.8 + - - +
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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