Contacts of the helix formed by residues 414 - 425 (chain D) in PDB entry 3RIK
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 414 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D VAL* 4.0 4.1 - - + +
352D VAL* 3.7 5.5 - - - +
353D ARG 3.2 6.2 + - - +
354D LEU* 3.3 11.6 - - + -
355D GLY* 2.9 30.0 + - - -
356D SER 4.2 0.9 + - - +
399D ASP* 2.8 37.4 + - - -
400D SER 3.3 10.8 + - - +
401D PRO 2.8 23.4 + - - +
403D ILE* 3.6 12.6 - - + +
412D TYR 4.4 5.4 - - - +
413D LYS* 1.3 71.3 - - - +
415D PRO* 1.4 73.0 - - + +
416D MET* 3.6 19.0 - - + +
417D PHE* 3.0 18.7 + - - +
418D TYR* 3.1 9.9 - - - -
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Residues in contact with PRO 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL 3.8 13.0 - - - +
48D ARG* 3.9 19.1 - - - +
355D GLY* 3.8 26.2 - - - +
356D SER 3.3 24.0 - - - +
357D TRP* 3.9 24.0 - - + -
360D GLY* 4.4 1.8 - - - -
414D GLN* 1.4 86.5 - - + +
416D MET* 1.3 56.2 + - - +
418D TYR* 3.0 10.8 + - + -
419D HIS* 2.8 39.2 + - + -
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Residues in contact with MET 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D VAL* 3.9 11.0 - - - -
353D ARG 5.7 0.2 - - - +
356D SER* 4.9 2.0 + - - +
359D ARG* 3.7 32.8 - - + +
360D GLY* 3.9 8.1 - - - +
363D TYR* 3.5 36.9 - - + -
399D ASP* 3.3 37.9 - - + +
400D SER 3.4 22.9 - - - +
401D PRO* 4.2 11.7 - - + -
414D GLN* 3.1 15.4 - - + +
415D PRO* 1.3 78.2 - - - +
417D PHE* 1.3 62.8 + - - +
419D HIS* 3.4 1.9 + - - +
420D LEU* 2.9 29.9 + - - +
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Residues in contact with PHE 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 6.1 1.6 - + - -
107D SER* 3.3 25.6 - - - -
108D TYR* 3.7 38.4 - + - -
113D GLY* 5.6 0.9 - - - -
114D ILE* 3.7 27.6 - - + +
401D PRO* 3.7 19.9 - - - +
402D ILE* 3.9 23.6 - - + -
413D LYS* 3.6 27.6 - - + -
414D GLN 3.0 16.6 + - - +
416D MET* 1.3 79.7 - - - +
418D TYR* 1.3 82.3 - + - +
420D LEU* 3.2 6.6 + - - +
421D GLY* 2.9 23.0 + - - -
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Residues in contact with TYR 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D CYS* 3.1 30.2 - - - +
24D ASP* 2.7 29.3 + - - -
26D PHE* 6.0 3.1 - + - -
42D SER* 4.1 17.0 - - - +
48D ARG* 3.4 40.8 - - + -
49D MET* 3.9 25.0 - - + +
357D TRP* 6.0 0.4 - - + -
413D LYS* 3.5 17.7 - - + +
414D GLN 3.1 28.0 - - - -
415D PRO* 3.0 5.9 + - + +
417D PHE* 1.3 91.3 - + - +
419D HIS* 1.3 69.4 + - + +
421D GLY* 2.9 11.8 + - - +
422D HIS* 3.0 21.4 + - - -
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Residues in contact with HIS 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D TRP* 3.2 47.6 - + - -
360D GLY* 3.1 34.4 + - - +
361D MET* 3.8 11.2 - - + -
363D TYR* 4.5 1.6 - - + -
364D SER* 2.7 31.2 + - - +
367D ILE* 5.3 0.7 - - - -
415D PRO* 2.8 30.2 + - + +
416D MET* 3.7 4.3 - - - +
418D TYR* 1.3 79.2 - - + +
420D LEU* 1.3 60.9 + - - +
422D HIS* 3.5 10.2 + - - +
423D PHE* 3.3 24.5 - - - -
461D LEU* 4.3 3.6 - - + -
489D ILE* 3.8 20.4 - - + +
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Residues in contact with LEU 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PHE* 5.1 9.4 - - + -
82D GLY 5.2 2.7 - - - +
114D ILE* 4.7 2.9 - - + -
116D TYR* 3.6 31.2 - - + +
363D TYR* 3.5 29.1 - - + +
367D ILE* 3.8 24.9 - - + -
378D TRP* 3.9 19.1 - - + +
380D ASP* 4.3 6.1 - - + +
401D PRO* 4.0 13.5 - - + -
416D MET 2.9 22.5 + - - +
417D PHE* 3.4 7.0 - - - +
419D HIS* 1.3 73.5 - - - +
421D GLY* 1.3 63.1 + - - +
423D PHE* 2.9 8.1 + - - +
424D SER* 2.8 26.6 + - - -
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Residues in contact with GLY 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D MET* 3.6 9.2 - - - +
114D ILE* 3.6 23.8 - - - +
417D PHE 2.9 12.6 + - - -
418D TYR 2.9 5.3 + - - -
420D LEU* 1.3 76.3 - - - +
422D HIS* 1.3 61.6 + - - +
423D PHE 3.0 0.2 - - - -
424D SER* 3.5 12.3 - - - -
425D LYS* 3.0 29.5 + - - +
426D PHE* 4.0 0.2 - - - -
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Residues in contact with HIS 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TYR* 3.3 29.5 - - + +
41D GLU 4.1 0.2 - - - -
42D SER* 2.9 28.6 + - - -
49D MET* 3.5 14.9 - - + +
418D TYR 3.0 29.0 + - - -
419D HIS 3.7 9.2 - - - +
420D LEU 3.1 0.6 - - - -
421D GLY* 1.3 76.4 - - - +
423D PHE* 1.3 59.0 + - + +
426D PHE* 3.4 12.8 - - - +
427D ILE* 4.9 0.5 - - - +
459D VAL* 3.9 6.4 - - + +
489D ILE* 3.3 49.5 - - + +
490D HIS 3.8 2.2 - - - -
491D THR* 2.8 43.3 + - - +
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Residues in contact with PHE 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PHE* 4.0 17.7 - - + -
364D SER* 3.7 27.1 - - - -
367D ILE* 3.6 28.3 - - + -
368D ILE* 3.5 35.4 - - + -
371D LEU* 4.2 2.9 - - + -
419D HIS 3.3 22.7 - - - -
420D LEU 2.9 4.5 + - - +
422D HIS* 1.3 78.3 - - - +
424D SER* 1.3 66.9 + - - +
425D LYS 3.1 2.0 + - - -
426D PHE 3.2 1.4 + - - -
427D ILE* 3.1 51.3 + - + +
447D VAL* 4.3 5.2 - - + -
459D VAL* 3.7 28.3 - - + -
489D ILE* 4.0 5.8 - - + -
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Residues in contact with SER 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PHE* 3.6 33.3 - - - -
114D ILE* 2.6 40.7 + - - +
115D GLY 4.0 2.6 - - - +
116D TYR* 3.8 14.6 - - - -
170D ARG* 2.7 31.7 + - - -
420D LEU* 2.8 20.4 + - - -
421D GLY* 3.5 0.9 - - - -
423D PHE* 1.3 74.0 - - - +
425D LYS* 1.3 52.4 + - - +
426D PHE 3.3 0.5 + - - -
427D ILE 4.0 4.0 + - - +
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Residues in contact with LYS 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 3.4 42.1 - - + +
27D ASP 5.1 1.4 + - - -
29D PRO* 6.0 2.4 - - - +
40D TYR* 4.9 4.7 - - - -
49D MET* 4.3 1.3 - - + -
111D GLU* 3.1 24.9 + - - +
113D GLY 2.8 29.2 + - - +
114D ILE* 3.3 14.6 - - - +
115D GLY 4.9 0.4 - - - +
170D ARG* 2.5 27.8 + - - +
421D GLY 3.0 18.1 + - - +
424D SER* 1.3 79.3 + - - +
426D PHE* 1.3 89.1 - - + +
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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