Contacts of the helix formed by residues 385 - 400 (chain B) in PDB entry 4G84
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 GLY 385 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B TYR 5.5 1.1 - - - -
356B SER 4.9 4.5 - - - -
357B VAL* 2.9 28.5 + - - +
358B ALA* 4.3 0.4 - - - +
383B SER 3.9 1.8 + - - -
384B ILE* 1.3 68.2 - - - +
386B VAL* 1.3 62.5 + - - -
387B GLU* 3.3 3.8 + - - -
388B ARG* 3.8 8.4 + - - +
389B ILE* 3.5 19.6 - - - +
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.7 15.7 - - + -
77B PHE* 3.6 18.6 - - + -
80B ILE* 4.0 9.2 - - + -
172B TYR* 3.3 44.7 + - + +
173B GLN* 5.1 1.1 - - - -
174B CYS* 4.8 5.4 - - + +
384B ILE* 2.9 12.7 + - + +
385B GLY* 1.3 71.0 - - - -
387B GLU* 1.3 60.8 + - - +
388B ARG 3.5 0.2 - - - -
389B ILE* 3.9 7.2 - - + +
390B PHE* 3.1 59.3 + - + -
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 5.7 0.5 + - - -
65B TYR* 3.2 18.4 + - - -
167B ARG* 3.6 27.6 + - - +
171B PHE* 3.5 30.2 - - + -
172B TYR* 3.0 33.8 + - - +
385B GLY 3.3 0.8 - - - -
386B VAL* 1.3 77.8 - - + +
388B ARG* 1.3 64.0 + - - +
389B ILE 3.5 0.2 + - - -
390B PHE* 3.7 24.6 + - - +
391B SER* 3.8 10.4 + - - -
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Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU* 4.5 11.7 - - - -
355B GLY* 4.0 25.7 - - - -
356B SER* 3.3 41.6 + - - +
357B VAL* 4.8 7.4 - - + -
385B GLY* 3.8 9.0 + - - +
386B VAL 3.5 0.2 - - - -
387B GLU* 1.3 77.7 - - - +
389B ILE* 1.3 60.7 + - - +
391B SER* 2.7 23.0 + - - +
392B ILE* 3.3 21.6 + - + +
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Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 4.2 13.7 - - + -
80B ILE* 5.4 0.4 - - + -
199B LEU* 5.0 3.4 - - + -
202B LEU* 3.8 33.4 - - + -
204B ILE* 4.2 17.0 - - + -
357B VAL* 3.3 33.0 - - + +
384B ILE* 4.0 17.9 - - + -
385B GLY 3.5 10.7 + - - +
386B VAL* 3.6 10.7 + - + +
387B GLU 3.3 0.4 - - - -
388B ARG* 1.3 75.0 - - - +
390B PHE* 1.3 66.4 + - - +
392B ILE* 3.3 7.4 + - + +
393B VAL* 2.9 39.4 + - + +
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Residues in contact with PHE 390 (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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65B TYR* 4.5 16.8 - + - -
69B GLN 6.0 0.2 - - - -
72B VAL* 3.6 12.7 - - + +
73B ARG* 3.7 31.9 - - + -
76B VAL* 3.6 28.5 - - + -
77B PHE* 3.7 18.8 - + - -
167B ARG* 5.5 2.9 - - - +
172B TYR* 4.6 2.0 - + - -
386B VAL* 3.1 50.8 + - + +
387B GLU* 3.8 29.6 - - - +
388B ARG 3.4 0.2 - - - -
389B ILE* 1.3 75.7 - - - +
391B SER* 1.3 57.5 + - - +
394B GLU* 3.0 30.5 + - - +
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Residues in contact with SER 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 6.2 1.8 - - - -
387B GLU 3.8 6.5 + - - -
388B ARG* 2.7 26.0 + - - +
390B PHE* 1.3 78.4 - - - +
392B ILE* 1.3 64.4 + - - +
394B GLU* 3.4 8.3 + - - +
395B GLN* 3.0 41.8 + - - +
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 3.6 35.9 - - + +
340B LEU* 3.4 33.7 - - + -
388B ARG* 3.3 25.5 + - + +
389B ILE* 3.3 9.8 + - + +
391B SER* 1.3 78.2 + - - +
393B VAL* 1.3 58.4 + - - +
395B GLN* 3.4 13.8 + - - +
396B ARG* 3.0 28.6 + - + +
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.1 14.8 - - + -
75B LYS* 4.0 27.8 - - + -
76B VAL* 4.1 8.7 - - + -
202B LEU* 4.6 5.6 - - + +
204B ILE* 3.9 16.2 - - + -
389B ILE* 2.9 37.2 + - + +
390B PHE 4.1 2.7 - - - +
392B ILE* 1.3 73.9 - - - +
394B GLU* 1.3 66.2 + - - +
396B ARG* 3.1 26.4 + - - +
397B LEU* 3.0 25.8 + - + +
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Residues in contact with GLU 394 (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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63B ARG* 5.7 1.4 + - - -
68B ARG* 3.9 18.1 + - - +
69B GLN* 4.2 25.3 + - - +
72B VAL* 4.0 26.7 - - + +
390B PHE 3.0 18.9 + - - +
391B SER* 3.8 7.5 - - - +
393B VAL* 1.3 76.7 - - - +
395B GLN* 1.3 58.1 + - + +
397B LEU* 3.2 5.0 + - - +
398B GLU* 2.9 58.7 + - + +
404B ILE* 5.1 1.3 - - + -
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Residues in contact with GLN 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B SER* 3.0 32.7 + - - +
392B ILE* 3.7 15.4 + - - +
394B GLU* 1.3 73.7 - - + +
396B ARG* 1.3 66.5 + - - +
398B GLU* 3.9 11.2 - - - +
399B ALA* 3.0 26.2 + - - +
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Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LYS* 4.1 24.9 - - - +
202B LEU 2.7 29.9 + - - -
203B GLN* 2.8 33.0 + - - +
204B ILE* 4.7 1.3 - - - +
392B ILE* 3.0 16.5 + - + +
393B VAL* 3.1 34.7 + - - +
395B GLN* 1.3 78.6 - - - +
397B LEU* 1.3 72.9 + - - +
399B ALA* 3.4 10.3 + - - +
400B LEU* 3.4 29.1 + - + +
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Residues in contact with LEU 397 (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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68B ARG* 5.3 0.2 - - - -
71B ALA 6.2 0.2 - - - -
72B VAL* 4.2 15.9 - - + -
75B LYS* 4.3 28.0 - - + -
393B VAL* 3.0 22.8 + - + +
394B GLU 3.2 6.5 + - - +
396B ARG* 1.3 90.5 - - + +
398B GLU* 1.3 61.0 + - - +
400B LEU* 3.3 23.9 + - + +
401B GLU 3.5 7.1 + - - -
402B GLU* 3.7 19.1 + - + +
404B ILE* 3.8 34.3 - - + -
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG* 3.2 33.1 + - - +
394B GLU* 2.9 49.5 + - + +
395B GLN* 4.1 8.4 - - - +
396B ARG 3.4 0.4 - - - -
397B LEU* 1.3 74.7 - - + +
399B ALA* 1.3 59.9 + - - +
401B GLU* 3.1 22.4 + - - +
402B GLU 5.5 0.4 - - - -
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Residues in contact with ALA 399 (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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395B GLN 3.0 19.1 + - - +
396B ARG* 3.7 6.5 - - - +
397B LEU 3.3 0.4 - - - -
398B GLU* 1.3 76.9 - - - +
400B LEU* 1.3 64.6 + - + +
401B GLU* 3.2 9.2 + - - +
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Residues in contact with LEU 400 (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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396B ARG* 3.4 21.9 + - + +
397B LEU* 3.3 18.6 + - + +
398B GLU 3.1 1.0 - - - -
399B ALA* 1.3 81.4 - - + +
401B GLU* 1.3 64.6 + - - +
402B GLU* 2.9 22.1 + - + +
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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