Contacts of the helix formed by residues 414 - 433 (chain A) in PDB entry 1C7G
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 TYR 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.4 25.6 - - + +
4A PRO* 2.5 40.9 + - - +
5A ALA* 4.6 0.4 - - - -
6A GLU* 4.3 5.7 + - - -
317A HIS* 3.5 17.7 - + - -
321A GLN* 3.9 24.0 + - + +
324A TYR* 3.6 49.5 - + + +
413A THR* 1.3 74.7 - - - +
415A ALA* 1.3 57.2 + - - +
417A MET* 3.0 9.2 + - - +
418A ASP* 2.9 32.6 + - - +
415B ALA* 4.1 24.7 - - + -
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A THR* 3.0 10.7 + - - +
414A TYR* 1.3 80.0 - - - +
416A HIS* 1.3 60.6 + - - +
418A ASP* 3.3 13.6 + - - +
419A VAL* 3.2 24.8 + - - +
5B ALA* 3.6 19.0 - - + +
6B GLU* 3.6 12.8 - - - +
414B TYR* 4.1 22.2 - - + -
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Residues in contact with HIS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 3.3 27.7 + + - -
45A ILE* 3.8 15.7 - - + +
411A VAL 4.9 0.4 - - - -
412A TYR* 3.6 27.8 - + + -
413A THR* 3.0 36.0 + - + +
415A ALA* 1.3 76.0 - - - +
417A MET* 1.3 66.9 + - + +
419A VAL* 3.1 12.9 + - - +
420A VAL* 3.0 19.1 + - - +
5B ALA* 4.1 6.1 - - + -
6B GLU* 2.7 37.5 + - + +
8B PHE 3.2 22.3 + - - -
9B ARG* 4.8 2.0 - - + -
10B ILE* 6.2 0.7 - - + -
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Residues in contact with MET 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 5.2 0.9 - - + -
47A LEU* 4.9 4.7 - - + -
321A GLN* 4.1 30.7 - - + +
324A TYR* 3.8 19.3 - - + -
325A LEU* 4.1 23.8 - - + +
407A ILE* 4.1 29.4 - - + -
412A TYR* 3.9 30.7 - - + -
413A THR 3.1 10.0 + - - +
414A TYR* 3.0 13.6 + - - +
416A HIS* 1.3 81.9 - - + +
418A ASP* 1.3 56.2 + - - +
420A VAL* 3.3 12.9 + - + +
421A ALA* 2.9 31.0 + - - +
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Residues in contact with ASP 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A TYR* 2.3 36.2 + - - -
328A LYS* 3.2 23.1 + - - +
414A TYR* 2.9 14.5 + - - +
415A ALA* 3.5 14.6 - - - +
416A HIS 3.2 0.2 - - - -
417A MET* 1.3 76.5 - - - +
419A VAL* 1.3 57.9 + - + +
421A ALA* 4.3 1.1 - - - -
422A ASP* 2.8 42.6 + - - +
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 4.5 12.1 - - + -
45A ILE* 4.1 15.3 - - + -
374A THR* 3.6 31.5 - - + +
376A VAL* 4.8 0.2 - - + -
415A ALA 3.2 14.8 + - - +
416A HIS* 3.1 10.0 + - - +
418A ASP* 1.3 78.3 - - + +
420A VAL* 1.3 61.1 + - - +
422A ASP* 4.4 3.2 - - - +
423A GLY 3.2 15.4 + - - -
5B ALA* 3.6 21.5 - - + -
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Residues in contact with VAL 420 (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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45A ILE* 4.6 10.3 - - + -
47A LEU* 4.5 18.2 - - + -
325A LEU* 4.0 23.8 - - + -
370A ILE* 6.4 0.2 - - - -
374A THR* 4.9 2.1 - - - +
376A VAL* 4.2 22.4 - - + -
405A LEU* 4.6 5.6 - - + -
416A HIS 3.0 18.6 - - - +
417A MET* 3.6 16.6 - - + +
419A VAL* 1.3 73.0 - - - +
421A ALA* 1.3 62.2 + - - +
423A GLY* 3.5 0.7 + - - -
424A ILE* 3.0 49.0 + - + +
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 4.0 13.5 - - + -
328A LYS* 3.6 34.8 - - + -
329A LEU* 4.1 13.8 - - + +
417A MET 2.9 19.6 + - - +
418A ASP 3.9 0.7 - - - +
420A VAL* 1.3 76.4 - - - +
422A ASP* 1.3 61.2 + - - +
424A ILE* 3.3 2.1 + - - +
425A ILE* 2.9 37.5 + - + +
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Residues in contact with ASP 422 (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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328A LYS* 3.1 23.5 + - - -
418A ASP* 2.8 29.3 + - - +
419A VAL* 4.4 3.3 - - - +
421A ALA* 1.3 73.6 - - - +
423A GLY* 1.3 61.6 + - - +
425A ILE* 3.5 11.5 + - - +
426A LYS* 3.1 24.4 + - - +
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Residues in contact with GLY 423 (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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373A GLU* 5.1 3.6 - - - +
374A THR* 3.4 30.2 - - - +
419A VAL 3.2 8.2 + - - -
421A ALA 3.2 0.8 - - - -
422A ASP* 1.3 80.1 - - - +
424A ILE* 1.3 60.6 + - - +
426A LYS* 3.5 8.6 + - - +
427A LEU* 3.2 27.6 + - - +
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Residues in contact with ILE 424 (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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329A LEU* 3.9 20.4 - - + -
334A VAL* 4.2 6.7 - - + -
347A LEU* 4.0 13.2 - - + -
352A PHE* 3.7 24.4 - - + -
370A ILE* 3.9 27.6 - - + -
374A THR* 6.2 0.4 - - + -
405A LEU* 4.0 26.5 - - + -
420A VAL* 3.0 38.5 + - + +
421A ALA 3.9 2.5 - - - +
423A GLY* 1.3 73.5 - - - +
425A ILE* 1.3 62.0 + - - +
427A LEU* 3.2 7.4 + - - +
428A TYR* 2.9 27.0 + - - +
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Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LYS* 3.9 19.7 - - + +
329A LEU* 4.4 5.4 - - + -
332A ALA* 3.7 32.8 - - + -
334A VAL* 4.3 9.4 - - + -
421A ALA* 2.9 28.9 + - + +
422A ASP* 3.8 13.2 - - - +
424A ILE* 1.3 77.2 - - - +
426A LYS* 1.3 62.8 + - - +
428A TYR* 3.2 9.0 + - + +
429A GLN* 3.0 43.5 + - + +
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Residues in contact with LYS 426 (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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373A GLU* 3.7 34.3 + - + +
422A ASP 3.1 18.2 + - - +
423A GLY* 3.7 6.7 - - - +
424A ILE 3.2 0.2 - - - -
425A ILE* 1.3 78.6 - - - +
427A LEU* 1.3 69.8 + - - +
429A GLN* 3.4 14.9 + - - +
430A HIS* 3.1 46.0 + - + +
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Residues in contact with LEU 427 (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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352A PHE* 4.1 11.6 - - + -
366A LEU* 4.4 5.8 - - + -
369A SER* 3.8 22.0 - - - +
370A ILE* 3.8 44.6 - - + +
373A GLU* 4.5 21.5 - - + +
423A GLY 3.2 18.1 + - - +
424A ILE* 3.2 10.5 + - - +
426A LYS* 1.3 85.2 - - - +
428A TYR* 1.3 58.5 + - - +
430A HIS* 3.0 8.7 + - + +
431A LYS* 2.8 27.5 + - - -
434A ILE* 4.5 10.9 - - + +
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Residues in contact with TYR 428 (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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332A ALA* 4.1 9.2 - - + -
333A GLY 3.1 30.3 + - - -
334A VAL* 3.6 20.0 - - + -
335A PRO* 3.5 21.0 - - + +
351A ARG 4.4 4.4 + - - -
352A PHE* 3.6 31.8 - + + -
424A ILE 2.9 13.4 + - - +
425A ILE* 3.2 9.2 + - + +
427A LEU* 1.3 77.4 - - - +
429A GLN* 1.3 62.4 + - + +
430A HIS 3.0 5.0 + - - -
431A LYS* 3.1 52.1 + - + +
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Residues in contact with GLN 429 (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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332A ALA* 5.9 1.8 - - - +
425A ILE* 3.0 35.1 + - + +
426A LYS* 3.7 13.6 - - - +
427A LEU 3.3 0.2 - - - -
428A TYR* 1.3 78.5 - - + +
430A HIS* 1.3 80.3 + - + +
431A LYS 3.7 0.4 - - - -
432A GLU* 3.6 8.9 - - - +
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Residues in contact with HIS 430 (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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426A LYS* 3.1 42.5 + - + +
427A LEU* 3.0 8.0 + - + +
428A TYR 3.0 0.4 - - - -
429A GLN* 1.3 101.9 + - + +
431A LYS* 1.3 54.9 + - - +
432A GLU* 3.1 15.7 - - - +
433A ASP* 2.8 48.6 + - + +
434A ILE* 4.1 1.7 + - - +
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Residues in contact with LYS 431 (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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351A ARG 4.9 2.0 - - - -
352A PHE* 2.9 35.0 - - + +
354A PRO* 3.8 23.8 - - + +
355A HIS* 2.8 24.7 + - - -
427A LEU 2.8 9.6 + - - +
428A TYR* 3.3 42.8 - - + +
429A GLN 3.7 0.2 - - - -
430A HIS* 1.3 77.1 - - - +
432A GLU* 1.3 75.4 + - + +
433A ASP 3.0 0.2 - - - -
434A ILE* 3.0 16.9 + - + +
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Residues in contact with GLU 432 (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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355A HIS* 3.5 27.5 - - + -
429A GLN 3.6 8.0 - - - +
430A HIS* 3.5 23.9 - - - +
431A LYS* 1.3 90.8 + - + +
433A ASP* 1.3 77.4 + - - +
434A ILE 3.4 1.2 + - - +
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Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A HIS* 2.8 32.5 + - + +
432A GLU* 1.3 89.1 - - - +
434A ILE* 1.3 62.4 + - + +
435A ARG* 3.2 14.7 + - - +
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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