Contacts of the helix formed by residues 414 - 433 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C ALA* 4.2 23.6 - - + -
3D TYR* 3.3 22.6 - - + +
4D PRO* 2.7 36.7 + - - +
6D GLU* 4.2 4.9 + - - -
317D HIS* 3.6 21.3 - + - -
320D LYS 4.6 0.2 + - - -
321D GLN* 3.7 35.6 + - + +
324D TYR* 3.7 44.6 - + + +
413D THR* 1.3 73.1 - - - +
415D ALA* 1.3 60.3 + - - +
417D MET* 3.1 7.0 + - - +
418D ASP* 2.9 32.7 + - - +
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Residues in contact with ALA 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C TYR 6.1 0.2 - - - +
5C ALA* 3.6 18.1 - - + +
6C GLU* 3.5 13.2 - - - +
414C TYR* 4.0 22.7 - - + -
413D THR* 3.1 10.7 + - - +
414D TYR* 1.3 81.1 - - - +
416D HIS* 1.3 61.0 + - - +
418D ASP* 3.3 12.7 + - - +
419D VAL* 3.2 26.5 + - - +
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Residues in contact with HIS 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ALA* 4.2 5.2 - - + -
6C GLU* 2.9 34.7 + - + +
8C PHE* 3.1 22.4 + + - -
9C ARG* 4.6 3.1 - - - +
10C ILE* 6.0 0.7 - - + -
44D TYR* 3.5 27.8 + + - -
45D ILE* 3.7 15.6 - - + +
411D VAL 4.6 0.7 - - - -
412D TYR* 3.5 31.9 - + + -
413D THR* 3.1 34.7 + - + +
414D TYR 3.1 0.2 - - - -
415D ALA* 1.3 77.6 - - - +
417D MET* 1.3 61.5 + - + +
419D VAL* 3.3 10.6 + - - +
420D VAL* 2.8 23.8 + - - +
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Residues in contact with MET 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 5.2 1.1 - - + -
47D LEU* 4.9 4.9 - - + -
321D GLN* 4.0 30.7 - - + +
324D TYR* 3.9 18.6 - - + -
325D LEU* 3.9 26.4 - - + +
407D ILE* 4.2 30.7 - - + -
412D TYR* 3.8 30.7 - - + -
413D THR 3.2 9.6 + - - +
414D TYR* 3.1 10.9 + - - +
416D HIS* 1.3 83.5 - - + +
418D ASP* 1.3 58.9 + - - +
420D VAL* 3.3 12.1 + - + +
421D ALA* 2.9 30.6 + - - +
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Residues in contact with ASP 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D TYR* 2.5 31.1 + - - -
328D LYS* 3.2 28.7 + - - +
414D TYR* 2.9 13.6 + - - +
415D ALA* 3.5 14.6 - - - +
416D HIS 3.2 0.4 - - - -
417D MET* 1.3 76.6 - - - +
419D VAL* 1.3 59.1 + - + +
422D ASP* 2.8 42.6 + - - +
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Residues in contact with VAL 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ALA* 3.6 20.6 - - + -
44D TYR* 4.4 14.8 - - + -
45D ILE* 4.0 16.4 - - + -
374D THR* 3.8 28.9 - - + +
376D VAL* 4.7 0.7 - - + -
415D ALA 3.2 16.7 + - - +
416D HIS* 3.5 9.2 - - - +
417D MET 3.2 0.4 - - - -
418D ASP* 1.3 78.9 - - + +
420D VAL* 1.3 62.1 + - - +
422D ASP* 4.3 2.5 - - - +
423D GLY 3.2 15.2 + - - -
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Residues in contact with VAL 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 4.6 7.2 - - + -
47D LEU* 4.5 14.8 - - + -
325D LEU* 3.9 25.8 - - + -
370D ILE* 6.3 0.2 - - - -
374D THR* 4.9 2.3 - - - +
376D VAL* 4.1 28.3 - - + -
405D LEU* 4.5 9.4 - - + -
416D HIS 2.8 20.0 - - - +
417D MET* 3.6 12.3 - - + +
419D VAL* 1.3 74.0 - - - +
421D ALA* 1.3 65.7 + - - +
423D GLY* 3.4 0.9 + - - -
424D ILE* 3.1 47.0 + - + +
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Residues in contact with ALA 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D LEU* 3.8 15.9 - - + -
328D LYS* 3.6 35.4 - - + -
329D LEU* 4.0 12.7 - - + +
417D MET 2.9 17.3 + - - +
418D ASP 4.1 0.2 - - - +
420D VAL* 1.3 80.4 - - - +
422D ASP* 1.3 62.0 + - - +
424D ILE* 3.4 1.4 + - - +
425D ILE* 3.0 31.9 + - + +
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Residues in contact with ASP 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D LYS* 3.0 27.7 + - - -
418D ASP* 2.8 32.4 + - - +
419D VAL* 4.3 3.0 - - - +
421D ALA* 1.3 73.2 - - - +
423D GLY* 1.3 63.3 + - - +
425D ILE* 3.4 11.1 + - - +
426D LYS* 3.1 22.9 + - - +
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Residues in contact with GLY 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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373D GLU* 5.1 3.3 - - - +
374D THR* 3.4 29.8 - - - +
419D VAL 3.2 8.9 + - - -
422D ASP* 1.3 80.7 - - - +
424D ILE* 1.3 57.1 + - - +
426D LYS* 3.4 8.9 + - - +
427D LEU* 3.1 31.6 + - - +
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Residues in contact with ILE 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D LEU* 3.9 21.5 - - + -
334D VAL* 4.2 4.5 - - + -
347D LEU* 4.2 9.6 - - + -
352D PHE* 3.5 25.4 - - + -
370D ILE* 3.9 33.0 - - + -
374D THR* 6.1 0.2 - - + -
405D LEU* 4.2 26.9 - - + -
420D VAL* 3.1 41.5 + - + +
421D ALA 4.0 2.7 - - - +
423D GLY* 1.3 74.8 - - - +
425D ILE* 1.3 59.7 + - - +
427D LEU* 3.3 5.9 + - - -
428D TYR* 3.0 25.5 + - - +
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Residues in contact with ILE 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D LYS* 4.1 16.6 - - - +
329D LEU* 4.4 3.6 - - + -
332D ALA* 3.6 33.9 - - + -
334D VAL* 4.2 9.2 - - + -
421D ALA* 3.0 30.7 + - + +
422D ASP* 3.8 14.4 - - - +
424D ILE* 1.3 75.6 - - - +
426D LYS* 1.3 64.2 + - - +
428D TYR* 3.3 8.8 + - + +
429D GLN* 3.1 43.6 + - + +
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Residues in contact with LYS 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D GLU* 3.8 33.9 + - + +
422D ASP 3.1 17.1 + - - +
423D GLY* 3.6 7.9 - - - +
425D ILE* 1.3 77.2 - - - +
427D LEU* 1.3 71.7 + - - +
429D GLN* 3.5 14.2 + - - +
430D HIS* 3.2 45.9 + - + +
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Residues in contact with LEU 427 (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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352D PHE* 4.0 10.7 - - + -
366D LEU* 4.4 6.1 - - + -
369D SER* 3.8 20.4 - - - +
370D ILE* 3.8 43.5 - - + +
373D GLU* 4.4 19.7 - - + +
423D GLY 3.1 17.9 + - - +
424D ILE* 3.7 9.9 - - - +
425D ILE 3.3 0.2 - - - -
426D LYS* 1.3 86.8 - - - +
428D TYR* 1.3 54.7 + - - +
430D HIS* 3.1 7.1 + - + +
431D LYS* 2.7 36.0 + - - -
434D ILE* 4.3 11.6 - - + +
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Residues in contact with TYR 428 (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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332D ALA* 4.1 10.3 - - + -
333D GLY* 3.2 28.9 + - - -
334D VAL* 4.0 17.9 - - + -
335D PRO* 3.5 21.3 - - + +
351D ARG 4.5 4.0 + - - -
352D PHE* 3.5 31.6 - + + -
424D ILE 3.0 13.8 + - - +
425D ILE* 3.4 9.6 - - + +
426D LYS 3.2 0.2 - - - -
427D LEU* 1.3 78.2 - - - +
429D GLN* 1.3 64.2 + - + +
430D HIS 2.9 5.7 + - - -
431D LYS* 3.0 51.3 + - + +
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Residues in contact with GLN 429 (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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332D ALA* 6.0 1.2 - - - +
425D ILE* 3.1 30.7 + - + +
426D LYS* 3.9 14.5 - - - +
427D LEU 3.3 0.4 - - - -
428D TYR* 1.3 84.9 - - + +
430D HIS* 1.3 79.0 + - + +
432D GLU* 3.7 8.0 - - - +
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Residues in contact with HIS 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D LYS* 3.2 42.7 + - + +
427D LEU* 3.1 8.8 + - + +
428D TYR 2.9 0.4 - - - -
429D GLN* 1.3 97.6 + - + +
431D LYS* 1.3 55.6 + - - +
432D GLU* 3.1 15.9 - - - -
433D ASP* 2.7 50.0 + - + +
434D ILE* 4.1 1.7 + - - +
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Residues in contact with LYS 431 (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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351D ARG 5.0 1.3 - - - -
352D PHE* 3.0 32.8 - - + +
354D PRO* 4.0 24.8 - - + +
355D HIS* 2.9 15.4 + - + +
427D LEU 2.7 11.2 + - - +
428D TYR* 3.2 40.6 - - + +
430D HIS* 1.3 77.2 - - - +
432D GLU* 1.3 73.7 + - + +
433D ASP 2.9 0.2 - - - -
434D ILE* 2.8 34.0 + - + +
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Residues in contact with GLU 432 (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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355D HIS* 3.6 28.8 - - + -
429D GLN 3.7 7.3 - - - +
430D HIS* 3.4 26.8 + - - +
431D LYS* 1.3 91.4 + - + +
433D ASP* 1.3 73.2 + - - +
434D ILE 3.3 0.7 - - - +
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Residues in contact with ASP 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D HIS* 2.7 32.0 + - + +
432D GLU* 1.3 88.8 - - - +
434D ILE* 1.3 63.5 + - + +
435D ARG* 3.2 15.2 + - - +
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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
------------------------------------------------------------
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