Contacts of the helix formed by residues 346 - 360 (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 GLN 346 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O GLU* 4.0 8.3 - - - +
113O ASP* 3.9 10.2 - - - +
143O TYR* 4.5 14.4 + - - -
144O SER* 5.3 8.3 + - - +
341P TYR* 3.2 26.9 + - + +
344P ARG* 3.1 32.0 + - - +
345P SER* 1.3 74.4 - - - +
347P HIS* 1.3 58.3 + - - +
348P GLU* 3.5 7.2 - - + -
349P LYS* 3.7 32.7 + - + +
350P ALA* 3.0 25.3 + - - +
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Residues in contact with HIS 347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308P TYR* 5.2 3.2 + - - -
342P SER* 3.4 25.0 + - - -
345P SER* 3.4 30.3 + - - -
346P GLN* 1.3 71.5 - - - +
348P GLU* 1.3 71.8 + - - +
350P ALA* 3.5 2.4 - - - +
351P ALA* 2.9 32.2 + - - +
374P GLU* 3.0 34.9 + - - +
377P GLU* 3.8 39.5 - - + +
378P MET* 4.2 9.1 - - + +
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Residues in contact with GLU 348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 3.6 52.9 - - + +
44D ILE* 3.3 19.3 - - + +
45D ALA* 4.7 4.0 - - - +
346P GLN* 5.0 4.7 - - + -
347P HIS* 1.3 87.3 + - - +
349P LYS* 1.3 62.6 + - + +
352P LEU* 3.3 16.6 + - - +
378P MET* 3.5 33.0 - - + +
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Residues in contact with LYS 349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D TRP* 4.6 21.2 - - + -
41D LEU* 5.0 5.1 - - + +
44D ILE* 5.7 0.7 - - - -
144O SER 4.5 14.9 + - - +
145O LYS 4.9 2.6 + - - -
146O LEU 4.0 15.8 + - - +
147O SER* 4.4 6.9 - - - +
341P TYR* 3.9 28.7 - - + +
346P GLN* 3.7 33.6 + - + +
347P HIS 3.4 0.2 - - - -
348P GLU* 1.3 77.6 - - + +
350P ALA* 1.3 65.5 + - - +
352P LEU* 3.1 20.9 + - - +
353P TYR* 3.0 56.6 + - - -
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Residues in contact with ALA 350 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338P GLY* 3.9 4.7 - - - +
341P TYR* 3.8 10.3 - - - +
342P SER* 3.6 35.9 - - - +
346P GLN 3.0 19.6 + - - +
347P HIS* 3.3 10.1 + - - +
349P LYS* 1.3 74.1 - - - +
351P ALA* 1.3 62.3 + - - +
353P TYR* 3.1 13.7 + - - +
354P PHE* 3.0 20.5 + - + -
374P GLU* 4.2 7.0 - - - +
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Residues in contact with ALA 351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 4.3 11.9 - - + -
347P HIS 2.9 19.8 + - - +
348P GLU 3.8 4.0 - - - +
350P ALA* 1.3 72.5 - - - +
352P LEU* 1.3 51.8 + - - +
354P PHE* 3.4 13.8 - - - +
355P GLN* 2.7 35.3 + - - +
371P MET* 4.2 7.9 - - + +
374P GLU* 3.8 17.9 - - + +
375P TYR* 4.8 16.6 - - + +
378P MET* 4.4 7.9 - - - -
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Residues in contact with LEU 352 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D TRP* 3.4 35.0 - - + +
44D ILE* 3.7 15.2 - - + +
47D LYS* 5.7 2.2 - - - +
348P GLU 3.3 11.0 + - - +
349P LYS* 3.1 30.4 + - - +
351P ALA* 1.3 76.9 - - - +
353P TYR* 1.3 77.6 + - + +
355P GLN* 3.0 17.5 + - + +
356P ARG* 2.8 33.4 + - + +
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Residues in contact with TYR 353 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147O SER* 3.7 11.4 - - - -
148O PHE* 3.0 26.1 + - + +
149O SER* 4.2 2.3 + - - -
328P LYS* 6.2 0.6 - - + +
334P CYS* 3.6 33.6 - - - +
337P ILE* 3.4 34.0 - - + +
338P GLY* 4.0 9.2 - - - -
341P TYR* 3.6 27.4 - + + -
349P LYS* 3.0 34.0 + - - +
350P ALA 3.1 6.7 + - - +
352P LEU* 1.3 84.7 - - + +
354P PHE* 1.3 53.0 + - - +
356P ARG* 3.1 31.9 + - + +
357P ALA* 2.8 34.3 + - - +
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Residues in contact with PHE 354 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335P CYS* 3.7 26.7 - - + -
338P GLY* 3.5 27.6 - - - -
339P ASN* 3.7 13.5 - - - -
350P ALA 3.0 28.2 + - - -
351P ALA* 3.4 6.3 - - - +
353P TYR* 1.3 72.3 - - - +
355P GLN* 1.3 64.9 + - - +
357P ALA* 3.0 6.5 + - - +
358P LEU* 3.0 28.4 + - - +
367P ALA* 4.3 11.3 - - + +
370P LEU* 3.6 39.5 - - + -
371P MET* 4.3 17.0 - - + -
374P GLU* 3.5 35.7 - - + -
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Residues in contact with GLN 355 (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* 4.8 1.9 - - - +
47D LYS* 3.3 47.8 + - - +
351P ALA 2.7 15.7 + - - +
352P LEU* 3.0 26.5 + - + +
354P PHE* 1.3 72.3 - - - +
356P ARG* 1.3 55.7 + - - +
358P LEU* 3.2 17.8 - - + +
359P LYS* 3.0 45.2 + - - +
371P MET* 3.5 18.5 - - + +
375P TYR* 3.5 11.3 + - - -
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Residues in contact with ARG 356 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M LEU* 5.2 9.5 - - + +
13M ASP* 5.1 7.9 + - - -
147O SER* 5.6 3.2 - - - -
328P LYS* 3.8 17.4 + - - +
329P TYR* 3.1 40.8 + - - -
334P CYS* 3.2 30.2 - - - -
337P ILE* 5.3 0.8 - - - +
352P LEU* 2.8 22.6 + - + +
353P TYR* 3.5 35.6 + - - +
355P GLN* 1.3 72.5 - - - +
357P ALA* 1.3 53.9 + - - +
359P LYS* 3.1 21.7 + - + +
360P LEU* 2.8 38.0 + - - +
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Residues in contact with ALA 357 (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* 3.2 31.6 - - + +
334P CYS* 3.6 24.1 - - + +
335P CYS* 4.1 10.5 - - + +
353P TYR 2.8 17.6 + - - +
354P PHE* 3.0 12.1 + - - +
356P ARG* 1.3 72.2 - - - +
358P LEU* 1.3 58.5 + - - +
360P LEU* 2.9 6.4 + - - +
361P ASN 2.8 20.4 + - - -
367P ALA* 4.5 5.8 - - + -
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Residues in contact with LEU 358 (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* 5.2 0.4 - - - -
354P PHE 3.0 8.8 + - - +
355P GLN* 3.2 36.6 - - + +
357P ALA* 1.3 73.4 - - - +
359P LYS* 1.3 64.7 + - + +
360P LEU 3.0 1.3 - - - -
361P ASN* 3.1 8.3 + - + +
362P PRO* 3.0 38.0 - - + +
364P TYR* 5.8 2.5 - - + +
367P ALA* 4.0 12.8 - - + +
368P TRP* 3.3 73.8 - - + +
371P MET* 3.8 17.9 - - + -
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Residues in contact with LYS 359 (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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47D LYS* 6.0 0.6 - - - +
7M ARG* 4.1 23.4 + - - +
12M LEU* 3.4 32.5 - - + +
17M ASP* 4.3 25.8 - - - +
131P ASP* 5.1 1.0 - - - +
355P GLN* 3.0 39.1 + - - +
356P ARG* 3.1 26.4 - - + +
358P LEU* 1.3 78.3 - - + +
360P LEU* 1.3 57.3 + - - +
361P ASN* 4.8 2.4 - - - +
362P PRO* 5.9 0.2 - - - +
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Residues in contact with LEU 360 (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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6M GLN* 2.8 42.4 - - + +
7M ARG* 4.1 14.4 - - + +
9M GLY* 4.0 25.4 - - - +
12M LEU* 4.4 14.8 - - + -
329P TYR* 3.8 34.3 - - + +
330P ARG 4.5 4.3 - - - +
331P VAL* 3.4 10.9 - - + +
334P CYS* 3.6 29.8 - - - -
356P ARG* 2.8 15.2 + - - +
357P ALA* 2.9 11.1 + - - +
359P LYS* 1.3 78.3 - - - +
361P ASN* 1.3 59.3 + - - +
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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
------------------------------------------------------------
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