Contacts of the helix formed by residues 349 - 364 (chain B) in PDB entry 2GB0
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 PHE 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 3.4 44.6 - + - -
61B TYR* 3.6 27.1 - + + -
64B LEU* 3.7 22.9 - - + -
65B ALA* 3.6 33.9 - - + -
68B SER* 3.3 7.2 + - - +
325B PHE* 3.5 24.9 - + + -
345B HIS 3.5 13.7 - - - -
346B GLY 3.0 6.8 + - - +
348B LYS* 1.3 95.3 - - + +
350B SER* 1.3 51.7 + - - +
351B SER 3.2 2.9 - - - -
352B GLY 2.9 4.0 + - - -
353B VAL* 2.7 47.8 + - + +
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Residues in contact with SER 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 3.6 21.2 + - - -
14B MET* 3.6 31.9 - - - +
17B ALA* 3.3 11.8 - - - +
72B TRP* 3.2 18.6 - - - -
346B GLY 3.3 3.0 + - - -
347B PHE* 2.9 31.4 + - - -
349B PHE* 1.3 77.6 - - - +
351B SER* 1.3 55.8 + - - +
353B VAL* 3.8 0.3 - - - +
354B GLY 2.8 23.7 + - - -
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Residues in contact with SER 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 4.5 1.1 - - - +
21B GLN* 4.6 3.6 - - - +
68B SER* 2.9 29.6 + - - -
71B LEU* 3.4 24.9 - - - +
72B TRP* 3.2 23.4 - - - -
156B TYR* 3.2 28.6 + - - -
350B SER* 1.3 79.2 + - - +
352B GLY* 1.3 69.6 + - - +
354B GLY* 3.2 9.9 + - - -
355B GLU* 3.3 8.7 + - - +
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Residues in contact with GLY 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.2 14.7 - - - +
67B ARG* 4.9 3.6 - - - -
68B SER* 3.1 16.4 + - - -
71B LEU* 3.7 13.6 - - - +
349B PHE 2.9 4.4 + - - -
351B SER* 1.3 82.9 + - - +
353B VAL* 1.3 61.9 + - - +
355B GLU* 3.1 6.7 + - - +
356B VAL* 3.0 24.1 + - - +
368B HIS* 4.8 0.5 - - - -
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET* 3.8 26.5 - - - -
64B LEU* 4.4 7.9 - - + -
325B PHE* 5.3 0.4 - - + -
327B ILE* 3.8 31.9 - - + -
339B ALA* 4.9 0.2 - - + -
342B PHE* 4.3 10.8 - - + -
349B PHE* 2.7 37.9 + - + +
350B SER 3.8 0.7 - - - +
352B GLY* 1.3 69.4 - - - +
354B GLY* 1.3 61.1 + - - +
356B VAL* 3.1 7.1 + - + +
357B LEU* 2.8 52.8 + - + +
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Residues in contact with GLY 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET 4.4 2.9 + - - -
17B ALA* 3.8 4.9 - - - -
18B ALA* 3.7 31.2 - - - -
21B GLN* 3.7 9.7 - - - +
350B SER 2.8 16.3 + - - -
351B SER 3.2 3.1 + - - -
352B GLY 3.2 0.2 - - - -
353B VAL* 1.3 77.2 - - - +
355B GLU* 1.3 56.1 + - - +
357B LEU* 3.9 0.4 - - - +
358B SER* 3.0 28.9 + - - -
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Residues in contact with GLU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLN* 3.7 26.4 + - - +
67B ARG* 2.6 48.4 + - - +
71B LEU* 4.3 6.0 - - + +
351B SER 3.3 10.7 + - - +
352B GLY 3.1 8.8 + - - +
354B GLY* 1.3 74.3 - - - +
356B VAL* 1.3 64.7 + - - +
358B SER* 3.3 4.2 + - - -
359B GLN* 3.1 40.7 + - + +
367B GLU* 4.2 5.4 - - - +
368B HIS* 2.9 25.9 + - + -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.4 8.7 - - + -
327B ILE* 3.8 27.8 - - + -
352B GLY 3.0 18.6 + - - +
353B VAL* 3.1 10.3 + - + +
355B GLU* 1.3 76.6 - - - +
357B LEU* 1.3 57.4 + - - +
359B GLN* 3.2 3.4 + - - +
360B LEU* 2.9 38.4 + - + +
366B THR* 3.8 17.5 - - + +
368B HIS* 3.6 36.3 - - + +
370B ILE* 4.2 13.5 - - + -
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET* 4.0 23.6 - - + +
18B ALA* 4.0 10.3 - - + -
198B ILE* 3.9 23.9 - - + +
200B SER* 5.0 0.4 - - - -
327B ILE* 4.1 18.8 - - + -
337B VAL* 3.6 24.0 - - + +
338B ILE 4.5 0.7 - - - +
339B ALA* 3.9 28.9 - - + -
353B VAL* 2.8 38.9 + - + +
354B GLY 3.9 3.8 - - - +
356B VAL* 1.3 72.3 - - - +
358B SER* 1.3 57.3 + - - +
360B LEU* 3.8 4.4 - - + +
361B ALA* 2.9 32.2 + - - +
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Residues in contact with SER 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 4.7 1.1 - - - +
21B GLN* 3.7 18.5 - - - +
22B LEU* 3.5 25.5 - - - +
25B GLN* 3.3 25.8 + - - -
198B ILE* 4.8 1.1 - - - +
354B GLY 3.0 17.6 + - - -
355B GLU* 3.5 6.3 - - - -
357B LEU* 1.3 78.6 - - - +
359B GLN* 1.3 58.2 + - - +
361B ALA* 3.4 0.9 + - - +
362B LEU* 3.0 36.5 + - - +
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Residues in contact with GLN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 6.3 1.1 - - - +
355B GLU* 3.1 29.3 + - + +
356B VAL 3.6 6.1 - - - +
358B SER* 1.3 74.6 - - - +
360B LEU* 1.3 60.4 + - - +
362B LEU* 4.9 3.4 - - - -
363B THR* 2.8 42.3 + - + +
365B LYS 3.1 11.4 - - - +
366B THR* 2.5 30.9 + - - +
367B GLU* 2.9 46.2 - - - +
368B HIS* 3.9 3.0 + - - -
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 4.2 9.2 - - + -
328B ASP* 4.3 11.9 - - - +
329B LEU* 4.0 18.4 - - + +
334B SER 5.0 1.9 - - - +
337B VAL* 3.8 28.7 - - + -
356B VAL* 2.9 37.3 + - + +
357B LEU 3.8 3.8 - - - +
359B GLN* 1.3 77.2 - - - +
361B ALA* 1.3 57.7 + - - +
364B GLY* 2.8 32.5 + - - +
365B LYS* 3.7 30.3 - - - +
366B THR* 4.2 7.4 - - + +
370B ILE* 4.1 15.0 - - + -
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.8 9.4 - - + -
22B LEU* 4.9 1.3 - - + -
196B LYS* 2.8 51.9 + - + +
198B ILE* 3.9 20.9 - - + -
337B VAL* 3.8 14.3 - - + +
357B LEU 2.9 18.6 + - - +
358B SER* 3.9 4.3 - - - +
360B LEU* 1.3 77.2 - - - +
362B LEU* 1.3 60.0 + - + +
364B GLY 4.8 0.2 + - - -
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.5 6.7 - - + -
22B LEU* 3.9 20.2 - - + -
25B GLN* 3.7 35.4 - - - +
27B VAL* 4.0 23.8 - - + -
196B LYS* 4.0 11.0 + - + +
358B SER* 3.0 25.4 + - - +
359B GLN* 4.9 1.1 - - - -
361B ALA* 1.3 79.1 - - - +
363B THR* 1.3 69.7 + - + +
364B GLY 3.9 0.2 - - - -
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Residues in contact with THR 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LYS* 5.9 0.7 - - - -
359B GLN* 2.8 30.3 + - + +
362B LEU* 1.3 85.2 - - + +
364B GLY* 1.3 59.2 + - - +
365B LYS* 2.9 40.7 + - - +
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Residues in contact with GLY 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LYS* 5.7 0.6 - - - +
329B LEU* 3.8 27.0 - - - +
334B SER* 5.2 3.6 - - - -
360B LEU* 2.8 33.3 + - - +
361B ALA 4.6 0.6 + - - -
362B LEU 3.9 0.4 - - - -
363B THR* 1.3 72.2 + - - +
365B LYS* 1.3 64.5 + - - +
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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