Contacts of the helix formed by residues 365 - 378 (chain P) in PDB entry 5G04
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 LEU 365 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240P GLU* 5.0 11.9 - - - +
301P ASP* 4.4 5.8 - - - +
363P ARG 3.5 6.7 + - - +
364P TYR* 1.3 99.7 - - + +
366P GLY* 1.3 73.4 + - - +
367P ALA 2.9 1.9 + - - -
368P TRP* 3.2 17.0 + - - +
369P THR* 3.8 7.6 + - - +
391P ALA* 4.6 2.1 - - - +
394P VAL* 4.9 4.1 - - - +
395P ASN* 3.6 39.0 - - - +
398P ASP* 4.3 9.5 - - + +
400P ARG* 6.3 0.4 - - - +
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Residues in contact with GLY 366 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301P ASP* 4.8 12.6 - - - -
305P ASN* 5.6 1.8 - - - -
335P CYS* 6.4 0.4 - - - -
364P TYR* 3.1 5.7 + - - -
365P LEU* 1.3 83.2 - - - +
367P ALA* 1.3 56.7 + - - +
369P THR* 2.9 15.8 - - - +
370P LEU* 2.9 39.8 + - - +
400P ARG* 4.6 9.0 - - - -
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Residues in contact with ALA 367 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331P VAL* 5.4 3.1 - - + -
335P CYS* 5.3 6.2 - - + +
354P PHE* 4.3 19.3 - - + +
357P ALA* 4.5 12.8 - - + -
358P LEU* 4.0 24.4 - - + +
364P TYR* 3.3 13.8 + - + +
365P LEU 2.9 1.4 + - - -
366P GLY* 1.3 72.8 - - - +
368P TRP* 1.3 57.2 + - + +
370P LEU* 3.7 8.0 - - - +
371P MET* 2.7 36.4 + - - +
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Residues in contact with TRP 368 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358P LEU* 3.3 34.7 - - + +
362P PRO* 3.8 26.5 + - + +
364P TYR 4.6 4.9 + - - -
365P LEU* 3.2 7.7 + - - +
367P ALA* 1.3 79.1 - - - +
369P THR* 1.3 61.6 + - - +
371P MET* 3.3 26.1 - - + +
372P GLY 3.1 15.8 + - - -
375P TYR* 5.9 0.4 - + - -
386P GLN* 5.3 5.8 - - + -
387P ALA* 3.4 40.2 - - + +
390P HIS* 3.3 46.3 - + + +
391P ALA* 3.6 22.2 - - + +
394P VAL* 4.2 16.8 - - + +
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Residues in contact with THR 369 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365P LEU 3.8 0.4 + - - +
366P GLY* 2.9 24.5 - - - +
368P TRP* 1.3 73.4 - - - +
370P LEU* 1.3 70.4 + - + +
372P GLY* 3.0 10.2 + - - -
373P HIS* 3.2 30.7 + - - +
388P TYR* 3.7 7.3 - - - -
391P ALA* 3.8 5.1 - - - +
398P ASP* 3.3 26.5 - - - +
400P ARG* 3.5 28.1 - - - +
401P ALA* 3.5 24.9 + - - -
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Residues in contact with LEU 370 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301P ASP* 5.0 4.7 - - - +
305P ASN* 3.7 26.7 - - - +
308P TYR* 6.2 4.7 - - + -
335P CYS* 5.1 4.9 - - - -
339P ASN* 3.7 18.8 - - - +
354P PHE* 3.6 34.1 - - + -
366P GLY* 2.9 31.4 + - - +
367P ALA* 3.7 3.8 - - - +
369P THR* 1.3 76.0 - - + +
371P MET* 1.3 58.9 + - - +
373P HIS* 2.8 39.8 + - + +
374P GLU* 3.3 20.7 + - - +
400P ARG* 5.8 4.7 - - - +
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Residues in contact with MET 371 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351P ALA* 4.2 12.5 - - + +
354P PHE* 4.3 7.3 - - + -
355P GLN* 3.5 40.4 - - + +
358P LEU* 3.8 17.7 - - + -
367P ALA 2.7 21.6 + - - +
368P TRP* 3.3 34.3 - - + +
370P LEU* 1.3 72.0 - - - +
372P GLY* 1.3 61.8 + - - +
374P GLU* 3.2 9.8 + - - +
375P TYR* 2.9 67.8 + - + +
387P ALA* 4.7 1.6 - - + -
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Residues in contact with GLY 372 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368P TRP 3.1 8.2 + - - -
369P THR 3.0 9.3 + - - -
371P MET* 1.3 75.8 - - - +
373P HIS* 1.3 51.7 + - - +
375P TYR* 2.9 6.7 + - - +
376P MET* 2.7 33.4 + - - +
384P ALA* 4.0 2.2 - - - +
387P ALA* 3.7 19.4 - - - +
388P TYR* 3.5 21.8 - - - -
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Residues in contact with HIS 373 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308P TYR* 6.6 0.4 - + - -
369P THR* 3.4 23.8 + - - -
370P LEU* 2.8 28.0 + - + +
372P GLY* 1.3 70.5 - - - -
374P GLU* 1.3 64.2 + - - +
376P MET* 3.0 6.3 - - - +
377P GLU* 2.8 43.8 + - - +
388P TYR* 2.9 43.0 + + - -
400P ARG* 4.3 25.3 + - + +
403P TYR* 6.0 3.6 - + - -
404P GLY* 5.1 1.8 - - - -
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Residues in contact with GLU 374 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308P TYR* 5.3 3.3 + - - -
342P SER* 3.4 24.2 + - - -
347P HIS* 3.0 35.3 + - - +
350P ALA* 4.4 0.7 - - - -
351P ALA* 3.8 24.2 - - + +
354P PHE* 3.5 31.7 - - + -
370P LEU* 3.5 21.5 - - - +
371P MET* 3.2 4.7 + - - +
372P GLY 3.0 0.8 + - - -
373P HIS* 1.3 84.3 - - - +
375P TYR* 1.3 61.7 + - - +
377P GLU* 3.1 17.4 + - - +
378P MET* 3.3 20.5 + - - +
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Residues in contact with TYR 375 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ILE 3.7 15.7 - - - -
47D LYS* 3.1 42.1 - - + +
48D ASP* 4.5 4.2 + - - -
351P ALA* 4.8 10.2 - - + +
355P GLN* 3.5 5.0 + - - -
368P TRP* 5.9 0.2 - + - -
371P MET* 2.9 63.0 + - + +
372P GLY 2.9 7.0 + - - +
374P GLU* 1.3 72.7 - - - +
376P MET* 1.3 64.6 + - - +
378P MET* 3.5 12.6 - - + +
379P LYS 3.3 3.5 + - - -
380P ASN* 3.2 39.4 + - - +
383P ALA* 3.6 22.0 - - + -
384P ALA* 3.8 8.5 - - - +
387P ALA* 3.9 16.4 - - + -
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Residues in contact with MET 376 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372P GLY 2.7 13.6 + - - +
373P HIS* 3.0 20.2 - - - +
375P TYR* 1.3 75.0 - - - +
377P GLU* 1.3 59.6 + - - +
379P LYS* 3.0 25.5 + - - +
380P ASN 5.0 0.7 - - - -
381P THR* 4.7 6.5 - - - +
384P ALA* 4.0 19.7 - - - +
388P TYR* 4.0 10.8 - - - +
404P GLY 4.6 0.2 - - - +
407P GLN* 3.6 44.9 - - + +
408P THR* 3.6 28.3 - - - +
411P ILE* 3.9 13.2 - - + -
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Residues in contact with GLU 377 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308P TYR* 5.6 1.7 + - - -
347P HIS* 3.8 40.7 - - + +
373P HIS* 2.8 41.3 + - - +
374P GLU* 3.1 11.1 + - - +
376P MET* 1.3 77.4 - - - +
378P MET* 1.3 57.6 + - - +
379P LYS* 3.0 21.8 + - - +
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Residues in contact with MET 378 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 3.3 28.0 - - + +
45D ALA* 3.7 22.5 - - + +
347P HIS* 4.2 13.8 - - + +
348P GLU* 3.5 50.7 - - - +
351P ALA* 4.4 4.5 - - - -
374P GLU 3.3 22.2 - - - +
375P TYR* 3.5 21.1 - - + +
377P GLU* 1.3 74.9 - - - +
379P LYS* 1.3 61.7 + - - +
380P ASN* 3.2 12.2 + - - +
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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
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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