Contacts of the helix formed by residues 435 - 455 (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 GLN 435 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A TYR* 3.2 25.7 + - + +
431A ALA 4.3 3.3 - - - +
432A PHE* 3.0 34.3 + - - +
434A ALA* 1.3 86.6 + - - +
436A THR* 1.3 58.7 + - - +
437A MET 3.4 2.2 - - - -
438A SER* 3.3 15.3 + - - +
439A LEU* 2.9 28.7 + - - +
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Residues in contact with THR 436 (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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421A LEU* 4.0 6.1 - - - +
424A THR* 3.5 17.6 - - - +
425A THR* 3.9 32.4 + - + +
428A ALA* 4.2 20.9 - - + -
432A PHE 3.6 10.8 - - - +
433A SER* 3.3 26.4 + - - +
434A ALA 3.5 1.6 - - - -
435A GLN* 1.3 78.1 - - - +
437A MET* 1.3 62.8 + - - +
439A LEU* 3.3 3.3 + - - -
440A TRP* 2.9 27.0 + - - +
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Residues in contact with MET 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 6.0 5.4 - - + +
421A LEU* 3.7 31.2 - - + -
434A ALA 5.0 3.5 + - - +
435A GLN 3.4 0.2 - - - -
436A THR* 1.3 83.4 + - - +
438A SER* 1.3 58.9 + - - +
440A TRP* 3.3 1.9 + - - +
441A PHE* 2.9 67.6 + - + -
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Residues in contact with SER 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 2.8 27.5 + - - -
82A ILE* 3.4 29.2 - - - +
434A ALA 5.6 0.4 + - - -
435A GLN* 3.3 17.9 + - - -
437A MET* 1.3 78.5 - - - +
439A LEU* 1.3 57.0 + - - +
441A PHE* 3.5 3.0 + - - -
442A LEU 2.8 16.5 + - - -
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Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 3.7 32.7 - - + +
275A PHE* 4.7 4.7 - - + -
278A MET* 3.9 26.2 - - + -
295A TYR* 3.8 20.4 - - + -
299A PHE* 3.8 22.0 - - + -
424A THR* 3.7 20.4 - - + -
428A ALA* 4.6 10.8 - - + -
435A GLN 2.9 17.0 + - - +
436A THR* 3.7 4.9 - - - +
438A SER* 1.3 76.0 - - - +
440A TRP* 1.3 64.1 - - - +
442A LEU* 3.2 24.8 + - + +
443A SER 3.7 3.3 + - - -
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Residues in contact with TRP 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 4.1 6.5 - - - -
302A SER* 3.2 23.8 - - - -
306A TRP* 3.6 32.9 + + - -
371A PHE* 4.3 7.0 - + - -
416A LEU* 3.7 14.6 - - + -
417A SER* 4.0 14.8 + - - -
420A GLY* 3.5 36.6 - - - -
421A LEU* 3.9 28.5 - - + +
424A THR* 3.5 19.7 - - - +
436A THR 2.9 15.6 + - - +
437A MET 3.7 1.6 - - - +
439A LEU* 1.3 77.3 - - - +
441A PHE* 1.3 94.0 + + - +
442A LEU 3.2 0.3 + - - -
443A SER* 2.9 28.8 + - - -
444A ASN* 4.1 1.6 + - - +
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Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.7 21.6 - + + -
421A LEU* 6.1 0.7 - - + -
437A MET* 2.9 54.3 + - + +
438A SER* 4.9 1.8 - - - -
440A TRP* 1.3 104.4 - + - +
442A LEU* 1.3 62.3 + - - +
443A SER 3.3 0.2 - - - -
444A ASN* 3.2 13.1 + - + +
445A ALA* 3.1 20.4 + - - +
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.4 29.6 - - + +
267A GLY* 6.5 0.2 - - - -
270A ILE* 4.3 23.3 - - + +
271A PRO* 4.0 28.0 - - + -
274A TYR* 4.8 8.5 - - + -
299A PHE* 3.8 21.5 - - + -
438A SER 2.8 14.7 + - - +
439A LEU* 3.3 23.3 - - + +
440A TRP 3.1 0.6 - - - -
441A PHE* 1.3 77.8 - - - +
443A SER* 1.3 57.1 + - - +
445A ALA* 4.4 0.9 - - + +
446A ALA* 2.9 33.9 + - + +
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 5.3 0.4 + - - -
299A PHE* 3.5 39.1 - - - -
302A SER* 2.6 36.5 + - - -
303A ALA* 3.5 11.4 - - - +
306A TRP* 4.1 1.4 - - - -
440A TRP* 2.9 23.6 + - - -
442A LEU* 1.3 78.0 - - - +
444A ASN* 1.3 61.2 + - - +
446A ALA* 4.6 0.9 - - - -
447A ALA* 3.2 22.7 + - - +
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Residues in contact with ASN 444 (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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306A TRP* 3.5 48.9 - - + +
310A GLU* 3.0 25.3 + - - +
440A TRP 5.1 0.7 - - - +
441A PHE* 3.2 14.5 + - + +
443A SER* 1.3 82.8 + - - +
445A ALA* 1.3 62.9 + - - +
447A ALA* 3.3 4.0 + - - +
448A GLN* 2.8 44.5 + - - +
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Residues in contact with ALA 445 (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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75A ALA* 3.5 22.7 - - + +
78A TYR* 3.4 48.0 - - + -
79A MET* 6.5 0.4 - - + -
441A PHE 3.1 10.3 + - - +
442A LEU* 3.2 5.6 + - + +
444A ASN* 1.3 78.9 + - - +
446A ALA* 1.3 64.4 + - - +
448A GLN* 3.2 4.4 + - - +
449A ALA* 3.1 19.8 + - - +
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLY* 3.4 27.8 - - - +
271A PRO* 4.1 12.6 - - + -
299A PHE* 4.8 4.7 - - + -
303A ALA* 5.2 4.0 - - + -
442A LEU* 2.9 20.2 + - + +
443A SER* 4.0 6.1 - - - +
445A ALA* 1.3 73.3 - - - +
447A ALA* 1.3 65.0 + - - +
449A ALA* 3.3 6.7 + - - +
450A ILE* 3.0 34.4 + - + +
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Residues in contact with ALA 447 (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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303A ALA* 3.1 31.4 - - - +
306A TRP* 3.8 7.6 - - + +
307A ALA* 3.4 18.8 - - - +
443A SER 3.2 13.6 + - - +
444A ASN 3.4 10.1 - - - +
445A ALA 3.2 0.2 - - - -
446A ALA* 1.3 78.7 - - - +
448A GLN* 1.3 57.4 + - + +
450A ILE* 3.4 7.1 + - - +
451A ASN* 2.8 34.5 + - - +
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Residues in contact with GLN 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 5.1 5.5 + - - -
70A MET 5.2 0.3 - - - +
71A SER 3.5 25.9 - - - +
74A GLY* 3.1 38.4 + - - -
75A ALA* 4.1 7.2 - - - +
310A GLU* 3.5 40.1 + - + +
444A ASN* 2.8 34.6 + - - +
445A ALA* 3.2 9.3 + - - +
447A ALA* 1.3 73.8 - - - +
449A ALA* 1.3 65.9 + - - +
451A ASN* 3.3 10.5 + - - +
452A ALA* 3.3 17.3 + - - +
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Residues in contact with ALA 449 (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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72A ILE* 5.0 0.4 - - - -
75A ALA* 4.1 5.1 - - + +
79A MET* 5.9 1.6 - - + -
263A VAL* 3.4 41.3 - - + +
264A GLY* 4.3 2.0 - - - -
267A GLY* 3.9 13.7 - - - -
445A ALA 3.1 13.3 + - - +
446A ALA* 3.3 8.0 + - - +
448A GLN* 1.3 77.5 - - - +
450A ILE* 1.3 60.0 + - - +
452A ALA* 3.5 5.5 + - - +
453A GLN* 2.9 29.1 + - - +
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Residues in contact with ILE 450 (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 GLY 5.0 5.6 - - - +
267A GLY 4.8 7.2 - - - +
268A ILE* 4.5 26.0 - - + -
303A ALA* 5.8 5.4 - - + -
307A ALA* 5.9 4.3 - - + -
446A ALA* 3.0 25.0 + - + +
447A ALA* 3.7 7.2 - - - +
449A ALA* 1.3 76.1 - - - +
451A ASN* 1.3 66.5 + - - +
453A GLN* 2.9 22.8 + - + +
454A LEU* 3.3 31.4 + - + +
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Residues in contact with ASN 451 (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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71A SER* 4.1 13.2 - - - +
307A ALA* 3.1 33.4 + - - +
310A GLU* 3.7 20.8 - - - +
311A GLN* 2.7 38.5 + - + +
314A THR* 5.2 1.4 + - - +
447A ALA 2.8 19.6 + - - -
448A GLN* 3.4 13.6 - - - +
450A ILE* 1.3 75.8 - - - +
452A ALA* 1.3 57.1 + - - +
454A LEU* 2.9 26.5 + - - +
455A VAL* 3.4 14.0 + - - +
466A TYR* 5.4 0.9 + - - -
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Residues in contact with ALA 452 (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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68A ALA* 3.7 13.6 - - - +
71A SER* 3.5 18.6 - - - -
72A ILE* 3.5 32.3 - - + -
260A ILE* 4.0 8.1 - - + +
448A GLN 3.3 3.7 + - - +
449A ALA 3.6 8.3 - - - +
450A ILE 3.1 0.6 - - - -
451A ASN* 1.3 79.2 - - - +
453A GLN* 1.3 67.9 + - - +
454A LEU 3.4 0.2 + - - -
455A VAL* 3.6 17.7 - - - +
456A ARG 5.1 0.2 + - - -
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Residues in contact with GLN 453 (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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260A ILE* 2.9 27.5 + - - +
261A SER* 3.7 19.6 + - - -
263A VAL* 5.0 0.4 - - - +
264A GLY* 3.2 20.9 - - - +
449A ALA* 2.9 25.5 + - - +
450A ILE* 2.9 12.1 + - + +
452A ALA* 1.3 84.9 - - - +
454A LEU* 1.3 67.5 + - + +
455A VAL 3.3 0.7 + - - -
456A ARG* 4.2 17.9 + - - +
457A PHE* 4.3 5.9 - - - -
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 5.7 3.4 - - + -
311A GLN* 4.4 11.0 - - - +
450A ILE* 3.3 34.1 + - + +
451A ASN* 2.9 14.1 + - - +
453A GLN* 1.3 85.5 - - + +
455A VAL* 1.3 65.7 + - - +
456A ARG 3.3 0.7 - - - -
457A PHE* 3.1 35.9 + - + +
466A TYR* 3.5 20.0 - - + +
470A ILE* 4.4 24.0 - - + -
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A HIS* 3.3 45.6 + - + +
67A LEU* 3.7 18.8 - - + -
68A ALA* 3.9 12.6 - - + +
71A SER* 3.9 17.0 - - - +
315A ILE* 4.7 11.2 - - + -
451A ASN 3.4 14.8 + - - +
452A ALA 3.6 14.1 - - - +
453A GLN 3.3 0.8 - - - -
454A LEU* 1.3 78.1 - - - +
456A ARG* 1.3 57.8 + - - +
458A TYR* 2.8 29.6 + - - +
466A TYR* 5.3 0.2 - - - -
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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
------------------------------------------------------------
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