Contacts of the helix formed by residues 434 - 451 (chain A) in PDB entry 2C6N
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 ALA 434 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A TYR* 3.8 15.3 - - - -
225A LEU* 3.8 6.9 - - + +
259A GLN 3.7 7.8 - - - +
261A TRP* 3.5 40.8 + - + +
429A ALA 3.2 2.2 + - - -
430A LEU 3.2 25.6 - - - +
432A LYS 3.5 0.2 - - - -
433A ILE* 1.3 79.0 - - - +
435A PHE* 1.3 58.0 + - - +
437A PRO* 3.4 16.0 - - - +
471A GLN* 4.4 5.5 + - - -
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Residues in contact with PHE 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLN* 3.1 44.6 + - + +
260A SER* 5.3 2.0 - - - -
431A GLU 3.6 17.2 + - - +
432A LYS 3.5 6.1 + - - +
433A ILE 2.9 0.6 + - - -
434A ALA* 1.3 78.8 - - - +
436A LEU* 1.3 70.8 + - + +
437A PRO 3.3 0.7 - - - -
438A PHE* 2.9 26.0 + + - +
439A GLY* 3.0 28.6 + - - -
498A TYR* 3.5 36.1 - + - -
501A TYR* 3.8 29.6 - + + -
502A PHE* 5.1 0.7 - - - -
505A PHE* 3.8 30.5 - + + -
705A LPR 4.5 10.1 - + - -
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 4.1 9.4 - - + -
218A LEU* 3.8 40.6 - - + +
221A LEU* 5.4 0.4 - - + -
222A TYR* 5.7 3.1 - - + -
432A LYS 3.4 18.8 - - - +
433A ILE* 3.1 24.7 + - + +
435A PHE* 1.3 78.9 - - + +
437A PRO* 1.3 73.0 - - + +
439A GLY 3.5 0.3 + - - -
440A TYR* 3.2 19.9 + - - +
502A PHE* 3.6 23.2 - - + -
505A PHE* 3.9 27.8 - - + -
506A VAL* 4.9 5.2 - - + -
570A LEU* 4.7 5.8 - - + -
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Residues in contact with PRO 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 3.3 27.6 - - + +
222A TYR* 3.6 28.3 - - + -
433A ILE 3.4 7.0 - - - +
434A ALA 3.4 16.6 - - - +
435A PHE 3.3 2.2 - - - -
436A LEU* 1.3 94.6 - - + +
438A PHE* 1.3 67.7 + - - +
440A TYR* 2.9 11.3 + - - +
441A LEU* 3.0 16.1 + - - +
470A TYR* 3.5 23.2 - - + +
471A GLN* 3.7 11.9 - - + -
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Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TRP* 4.2 13.7 - + + -
259A GLN* 3.4 33.0 - - + -
435A PHE* 2.9 14.8 + + - +
437A PRO* 1.3 74.5 - - - +
439A GLY* 1.3 65.8 + - - +
441A LEU* 2.9 27.9 + - + +
442A VAL* 3.1 31.6 + - + +
463A TRP* 4.3 7.2 - + - -
467A ARG* 2.8 33.7 - - - -
471A GLN* 3.4 25.4 - - - +
489A LYS* 4.3 15.3 - - + -
498A TYR* 3.3 33.7 - + - -
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Residues in contact with GLY 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PHE* 3.0 24.3 + - - -
436A LEU 4.0 2.2 - - - -
438A PHE* 1.3 80.2 - - - +
440A TYR* 1.3 60.8 + - - +
442A VAL* 4.4 1.9 + - - +
443A ASP 4.7 0.3 + - - -
498A TYR* 3.7 35.7 - - - +
499A ILE* 4.2 6.2 + - - +
502A PHE* 4.1 17.5 - - - +
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Residues in contact with TYR 440 (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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208A GLU 4.6 1.9 + - - -
211A LEU* 3.9 28.5 - - + -
212A GLU* 3.3 33.2 + - + +
215A TYR* 4.4 14.4 - + + -
436A LEU 3.2 10.8 + - - +
437A PRO 2.9 10.2 + - - +
439A GLY* 1.3 79.6 - - - +
441A LEU* 1.3 55.2 + - - +
442A VAL 3.5 0.3 + - - -
443A ASP 3.9 1.6 + - - -
444A GLN* 2.8 57.3 + - + +
470A TYR* 3.4 46.7 + + - -
499A ILE* 4.3 10.3 - - + +
502A PHE* 3.8 31.9 - + + -
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PRO 3.0 10.7 + - - +
438A PHE* 2.9 19.2 + - + +
440A TYR* 1.3 77.2 - - - +
442A VAL* 1.3 92.3 + - + +
444A GLN* 2.7 36.5 + - - +
445A TRP* 2.9 5.9 + - - +
463A TRP* 4.1 15.5 - - + -
466A LEU* 3.4 20.9 - - + +
467A ARG* 3.3 45.3 - - + +
470A TYR* 4.4 17.5 - - + -
471A GLN* 4.0 10.3 - - + +
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Residues in contact with VAL 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 3.1 34.1 + - + +
439A GLY 4.7 0.2 - - - +
440A TYR 3.5 0.6 + - - -
441A LEU* 1.3 97.3 - - + +
443A ASP* 1.3 68.1 + - - +
445A TRP* 3.0 18.1 + - + +
446A ARG* 3.1 23.0 + - + +
463A TRP* 4.2 13.7 - - + -
489A LYS* 5.6 3.4 - - + -
491A HIS* 5.9 0.7 - - + -
492A VAL* 5.2 9.2 - - + -
498A TYR* 3.4 41.1 - - + -
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Residues in contact with ASP 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 4.0 11.8 - - - +
439A GLY 4.7 0.4 + - - -
440A TYR 3.9 4.8 + - - +
441A LEU 3.5 0.4 - - - -
442A VAL* 1.3 75.8 - - - +
444A GLN* 1.3 59.3 + - - +
445A TRP 3.2 0.2 - - - -
446A ARG* 3.4 21.5 + - - -
447A TRP* 2.9 57.9 + - + -
497A PRO* 4.0 2.2 - - - +
498A TYR* 2.7 41.6 + - - +
499A ILE* 3.1 33.0 + - + +
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Residues in contact with GLN 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 5.6 0.2 - - - +
440A TYR* 2.8 68.9 + - + +
441A LEU* 2.7 15.9 + - - +
443A ASP* 1.3 82.4 - - - +
445A TRP* 1.3 60.5 + - - +
447A TRP* 3.4 35.4 + - - +
448A GLY 3.7 3.1 + - - -
453A ARG* 3.1 30.7 + - - -
466A LEU* 4.0 15.7 - - + +
470A TYR* 4.6 7.9 + - + +
499A ILE* 5.0 0.8 - - - +
710B ACT 5.6 0.2 - - - -
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Residues in contact with TRP 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 4.2 10.8 - + - -
441A LEU 2.9 6.8 + - - +
442A VAL* 3.3 11.4 - - + +
444A GLN* 1.3 78.3 - - - +
446A ARG* 1.3 93.2 + - + +
448A GLY* 3.2 5.4 + - - -
449A VAL* 3.2 40.7 + - + +
453A ARG* 4.3 1.8 + - - +
454A THR* 4.2 8.8 + - + +
459A TYR* 3.2 29.0 + + - -
462A ASP* 4.0 11.4 - - + -
463A TRP* 3.8 42.1 - + + +
466A LEU* 3.4 16.5 - - + +
484A PHE* 3.9 27.4 - + - -
486A ALA* 3.7 29.2 - - + -
492A VAL* 4.3 14.8 - - + -
710B ACT 5.2 0.9 - - - -
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.4 20.0 + - - +
198A TRP* 3.6 27.4 - - + -
442A VAL* 3.1 21.6 + - - +
443A ASP* 3.4 27.7 + - - +
444A GLN 3.4 0.2 - - - -
445A TRP* 1.3 98.2 - - + +
447A TRP* 1.3 64.6 + - + +
448A GLY 2.8 5.4 - - - -
449A VAL* 2.7 17.4 + - + +
450A PHE* 2.9 22.9 + - + +
491A HIS* 3.4 22.0 + - - +
492A VAL* 3.8 14.3 - - + +
495A VAL* 4.1 4.4 - - - +
496A THR 2.2 39.8 + - - +
497A PRO 3.9 0.2 - - - -
498A TYR* 3.7 9.3 - - - +
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Residues in contact with TRP 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASP* 4.7 0.7 - - - +
195A GLY* 4.1 15.7 + - - -
198A TRP* 4.6 12.5 - + - +
199A ARG* 3.2 43.5 + - + +
207A PHE* 4.2 8.3 - + - -
208A GLU* 3.8 33.9 - - + -
211A LEU* 4.3 11.4 - - + -
443A ASP* 2.9 40.9 + - + +
444A GLN* 3.4 33.2 - - - +
446A ARG* 1.3 72.2 - - + +
448A GLY* 1.3 56.0 + - - +
450A PHE* 3.8 8.0 + + - +
451A SER* 3.1 28.6 + - - -
453A ARG* 4.4 7.4 - - - +
499A ILE* 3.7 42.5 - - + +
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Residues in contact with GLY 448 (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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445A TRP 3.2 5.3 + - - -
446A ARG 2.7 2.0 + - - -
447A TRP* 1.3 79.8 - - - +
449A VAL* 1.3 54.3 + - - +
451A SER* 3.6 7.9 - - - -
452A GLY 3.1 3.1 + - - -
453A ARG* 2.7 63.2 + - - +
454A THR* 2.7 12.8 + - - -
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Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 4.3 8.3 - - + -
179A THR* 4.2 22.6 - - + +
445A TRP* 3.2 52.6 + - + +
446A ARG* 2.7 16.2 + - + +
448A GLY* 1.3 70.8 - - - -
450A PHE* 1.3 63.5 + - + +
452A GLY* 3.2 13.0 + - - -
454A THR* 3.6 20.4 - - + +
459A TYR* 3.7 29.6 - - + +
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Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 4.3 8.1 - - - -
178A PHE* 4.0 21.1 - + - -
179A THR* 3.7 30.1 - - + -
182A SER* 4.5 1.3 - - - -
183A ASN* 3.2 29.6 + - - +
193A ASP* 3.0 22.2 - - - +
194A THR* 3.8 20.2 - - + -
195A GLY* 3.7 31.6 - - - +
198A TRP* 3.4 43.7 - + - -
446A ARG* 2.9 27.1 + - + +
447A TRP* 4.0 3.1 - - - +
449A VAL* 1.3 80.1 - - + +
451A SER* 1.3 57.0 + - - +
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Residues in contact with SER 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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192A THR* 6.1 0.2 - - - -
193A ASP* 3.6 18.4 - - - -
199A ARG* 6.0 2.0 - - - -
447A TRP 3.1 19.2 + - - -
448A GLY* 3.4 2.8 + - - -
449A VAL 3.1 0.2 - - - -
450A PHE* 1.3 79.4 - - - +
452A GLY* 1.3 58.5 + - - +
453A ARG* 3.3 20.1 + - - +
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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
------------------------------------------------------------
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