Contacts of the helix formed by residues 453 - 468 (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 HIS 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A GLY 5.6 1.6 - - - +
451A SER* 3.2 1.4 - - - -
452A TYR* 1.3 103.2 - + + +
454A GLY* 1.3 64.1 + - - +
455A ASP* 3.1 8.5 - - - -
456A LEU* 3.0 23.1 + - + +
457A MET* 3.1 22.6 + - + +
567A ASP* 3.6 26.0 - - - -
826A GLU* 4.0 0.7 - - - -
832A LYS* 3.5 38.2 - - + +
833A ASP 3.5 24.0 + - - -
834A THR* 4.5 1.6 - - - -
835A PRO* 3.9 8.7 - - + +
941A LYS* 2.9 24.8 + - - -
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Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 3.2 31.4 - - - -
451A SER* 2.9 11.9 + - - -
453A HIS* 1.3 76.3 - - - +
455A ASP* 1.3 56.4 + - - +
457A MET* 3.5 12.6 - - - +
458A GLU* 2.8 38.5 + - - +
1980A GOL 3.2 3.2 + - - -
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Residues in contact with ASP 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A MET* 4.2 2.7 - - + +
227A GLY* 3.6 24.0 - - - +
230A HIS* 4.7 3.6 + - - +
453A HIS 3.4 2.8 - - - -
454A GLY* 1.3 76.4 - - - +
456A LEU* 1.3 58.5 + - - -
458A GLU* 3.3 1.6 + - - +
459A ARG* 2.7 46.3 + - - +
821A TYR* 4.4 7.3 + - - -
826A GLU* 4.1 3.7 - - - +
941A LYS* 2.8 32.0 + - - -
944A HIS* 2.8 25.9 + - + +
1980A GOL 3.0 27.7 + - - +
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Residues in contact with LEU 456 (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* 4.3 3.6 - - + -
453A HIS* 3.0 27.8 + - + +
455A ASP* 1.3 82.6 + - - +
457A MET* 1.3 58.8 + - + +
459A ARG* 3.6 29.8 - - - +
460A SER* 2.8 33.8 + - - -
826A GLU* 3.6 33.9 - - + +
828A LEU 4.3 0.2 - - - +
829A PRO* 4.3 2.3 - - + +
830A THR* 3.4 50.9 - - + +
832A LYS* 4.0 13.9 - - + +
941A LYS* 4.0 3.8 - - - +
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Residues in contact with MET 457 (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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254A CYS* 3.7 23.3 - - - -
301A GLY* 4.0 21.8 - - - +
303A ASP* 3.5 33.9 - - + +
304A ALA* 4.0 24.7 - - + +
307A TRP* 4.1 7.4 - - - -
448A SER* 4.7 4.7 - - - +
451A SER* 3.9 19.1 - - - +
453A HIS* 3.1 19.0 + - + +
454A GLY* 3.5 16.8 - - - +
456A LEU* 1.3 77.1 - - + +
458A GLU* 1.3 59.6 + - - +
460A SER* 3.5 2.9 + - - -
461A LEU* 3.2 21.7 + - - +
1986A MGD 4.0 8.7 - - - +
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Residues in contact with GLU 458 (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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224A THR 4.2 0.5 - - - +
225A TYR* 3.1 35.7 - - - +
226A MET 4.2 1.5 + - - -
227A GLY* 2.9 28.3 + - - -
228A ALA* 3.6 1.2 + - - +
444A ILE* 4.3 18.4 - - + -
448A SER* 2.5 39.7 + - - +
449A ALA* 4.1 2.6 + - - -
454A GLY 2.8 21.5 + - - +
455A ASP 3.6 2.7 - - - +
457A MET* 1.3 70.4 - - - +
459A ARG* 1.3 66.4 + - - +
460A SER 3.1 1.8 - - - -
461A LEU* 3.1 7.1 + - - +
462A PHE* 2.9 35.2 + - + -
1980A GOL 4.7 0.7 + - - -
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Residues in contact with ARG 459 (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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227A GLY* 3.8 11.4 - - - -
230A HIS* 5.0 4.9 - - - +
231A THR* 3.6 25.8 + - - +
455A ASP* 2.7 33.5 + - - +
456A LEU* 3.5 24.6 + - - +
458A GLU* 1.3 72.3 - - - +
460A SER* 1.3 56.8 + - - +
462A PHE* 3.3 2.5 + - - -
463A LEU* 2.9 28.1 + - - +
813A GLN 5.2 1.6 + - - -
814A PHE* 2.9 38.6 + - + +
816A LEU* 3.6 29.6 - - - +
821A TYR* 4.3 5.0 - - - -
826A GLU* 2.9 23.6 + - - +
827A SER 3.1 16.0 + - - -
828A LEU 3.5 6.1 + - - -
829A PRO* 3.5 19.8 - - + +
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Residues in contact with SER 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA* 3.5 30.2 - - - +
307A TRP* 3.5 17.1 - - - +
308A LEU* 3.7 11.6 - - - +
311A SER* 4.3 2.6 + - - -
456A LEU 2.8 20.7 + - - -
457A MET 3.7 5.2 - - - -
458A GLU 3.1 0.6 - - - -
459A ARG* 1.3 73.3 - - - +
461A LEU* 1.3 67.3 + - - +
463A LEU* 3.2 6.9 + - - +
464A ALA* 3.2 16.8 + - - +
829A PRO* 3.4 18.7 - - - +
830A THR 4.0 0.7 + - - -
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 4.0 12.8 - - + -
307A TRP* 3.5 51.4 - - + +
442A SER* 4.3 11.9 - - - +
444A ILE* 3.8 29.4 - - + -
457A MET 3.2 13.9 + - - +
458A GLU* 3.1 8.8 + - - +
460A SER* 1.3 75.9 - - - +
462A PHE* 1.3 81.9 + - + +
464A ALA* 3.1 5.4 + - - +
465A MET* 3.0 44.3 + - + +
478A ALA* 5.1 1.1 - - + -
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Residues in contact with PHE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLY 4.3 3.6 - - - -
228A ALA* 3.7 31.0 - - + -
231A THR* 4.4 2.7 - - + -
232A PHE* 3.6 35.2 - + + -
237A MET* 5.7 0.7 - - + -
444A ILE* 3.9 7.4 - - + -
458A GLU* 2.9 37.2 + - + +
459A ARG* 3.8 4.5 - - - +
461A LEU* 1.3 86.5 - - + +
463A LEU* 1.3 57.0 + - - +
465A MET* 3.6 10.1 - - + +
466A ALA* 2.8 30.5 + - - +
471A TRP* 3.7 3.0 - + - -
478A ALA* 3.6 32.3 - - + -
479A PHE* 3.9 15.9 - + - -
814A PHE* 3.5 11.8 - - + -
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 4.0 17.5 - - + -
311A SER* 3.8 19.1 - - - +
331A LEU* 4.2 11.2 - - + -
405A LEU* 3.7 45.3 - - + -
459A ARG 2.9 13.6 + - - +
460A SER* 3.5 8.7 - - - +
461A LEU 3.2 0.4 - - - -
462A PHE* 1.3 75.3 - - - +
464A ALA* 1.3 57.9 + - - +
466A ALA* 3.3 2.9 + - + +
467A LEU* 3.0 45.8 + - + +
814A PHE* 3.2 29.8 - - + -
829A PRO* 4.4 8.5 - - + -
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Residues in contact with ALA 464 (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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307A TRP* 3.6 33.2 - - + +
310A LEU* 4.6 2.5 - - + -
311A SER* 3.6 12.0 + - - +
314A MET* 3.3 28.6 - - + +
435A VAL* 4.0 3.3 - - + +
460A SER 3.2 4.7 + - - +
461A LEU 3.1 9.1 + - - +
463A LEU* 1.3 79.0 - - - +
465A MET* 1.3 54.4 + - - +
468A SER* 2.7 32.8 + - - -
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Residues in contact with MET 465 (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* 4.5 0.9 - - + -
307A TRP* 3.7 33.0 - - + -
435A VAL* 4.7 4.3 - - + -
440A THR* 3.7 25.4 - - + +
442A SER* 3.7 22.0 - - - +
461A LEU* 3.0 27.2 + - + +
462A PHE* 3.3 13.2 + - + +
464A ALA* 1.3 75.0 - - - +
466A ALA* 1.3 63.3 + - - +
468A SER* 3.2 5.0 + - - -
469A GLY 3.0 3.1 + - - -
470A ASN* 2.8 59.8 + - - +
471A TRP* 4.3 9.1 - - + -
477A GLY 5.9 2.0 - - - +
478A ALA* 6.5 0.2 - - + -
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Residues in contact with ALA 466 (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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324A PHE* 3.2 18.7 - - - +
325A VAL* 3.4 10.8 - - + +
329A THR* 4.0 9.6 - - + -
331A LEU* 5.7 0.9 - - + -
462A PHE 2.8 20.9 + - - +
463A LEU* 3.3 8.7 + - + +
465A MET* 1.3 74.1 - - - +
467A LEU* 1.3 62.4 + - - +
469A GLY 3.1 9.7 + - - -
471A TRP* 3.6 27.7 - - + -
814A PHE* 3.8 16.4 - - + -
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Residues in contact with LEU 467 (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* 3.4 42.2 - - - +
314A MET* 3.9 14.1 - - + -
315A ILE* 3.9 31.9 - - + -
320A PHE* 3.2 19.6 - - + -
321A ASP 2.8 28.8 + - - -
325A VAL* 3.7 9.9 - - + -
331A LEU* 3.8 25.1 - - + -
402A PHE* 4.2 5.2 - - + -
463A LEU* 3.0 29.3 + - + +
466A ALA* 1.3 77.7 - - - +
468A SER* 1.3 57.6 + - - +
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Residues in contact with SER 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A MET* 3.9 3.6 - - - -
319A LEU 5.6 0.2 - - - -
321A ASP* 4.1 9.9 - - - +
435A VAL* 3.2 35.4 - - - +
436A ALA* 3.8 17.8 - - - +
464A ALA 2.7 21.8 + - - -
465A MET* 3.2 8.7 + - - -
467A LEU* 1.3 77.7 - - - +
469A GLY* 1.3 60.7 + - - +
470A ASN* 3.0 19.2 + - - +
473A LYS* 5.1 0.9 + - - -
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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