Contacts of the helix formed by residues 392 - 406 (chain B) in PDB entry 5F2R
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 GLU 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B CYS* 4.1 16.8 - - - -
52B ILE* 4.0 16.1 - - + +
60B ARG* 2.8 54.9 + - - +
61B ILE* 4.8 5.1 - - + +
367B ARG* 4.5 4.5 + - - -
388B ILE* 4.5 4.3 - - + +
389B ASN* 2.7 41.1 + - + +
391B ASP* 1.3 87.5 - - - +
393B ALA* 1.3 51.3 + - - -
394B VAL 3.3 2.2 - - - -
395B ALA* 3.2 8.0 + - - +
396B TYR* 2.8 34.0 + - - +
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA 3.8 2.6 - - - +
205B ALA* 4.2 20.4 - - + -
208B ALA* 3.4 10.4 - - + +
209B TYR* 4.7 12.3 - - + -
361B LEU 5.0 4.5 - - - +
362B VAL* 5.0 1.8 - - + -
388B ILE* 3.8 20.0 - - + -
389B ASN 2.9 10.5 + - - +
390B PRO* 3.6 14.1 + - + +
392B GLU* 1.3 76.8 - - - +
394B VAL* 1.3 61.6 + - - +
396B TYR* 3.2 2.6 + - - +
397B GLY 3.0 19.1 + - - -
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 3.7 23.8 - - + +
171B THR* 3.3 35.4 - - + +
201B GLU* 3.7 33.7 - - + +
204B ALA* 3.5 11.4 - - + +
205B ALA* 4.3 3.4 - - + +
224B ASP* 5.6 0.4 - - - +
362B VAL* 3.7 28.0 - - + -
390B PRO 4.8 1.1 + - - +
391B ASP 5.3 1.5 - - - +
392B GLU 3.3 0.2 - - - -
393B ALA* 1.3 78.8 - - - +
395B ALA* 1.3 62.7 + - - +
397B GLY 3.2 0.3 + - - -
398B ALA* 3.0 19.4 + - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLY 4.1 7.1 - - - +
34B ASP* 3.9 9.9 + - + +
41B CYS* 3.5 53.6 - - + +
42B VAL* 4.2 1.3 - - - +
43B GLY 4.5 0.4 + - - +
52B ILE* 4.4 6.1 - - + -
392B GLU 3.2 3.1 + - - +
394B VAL* 1.3 79.3 - - - +
396B TYR* 1.3 57.0 + - - +
398B ALA* 3.3 9.0 + - - +
399B ALA* 2.9 30.4 + - - +
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Residues in contact with TYR 396 (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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49B ARG* 5.7 1.6 - - - +
50B VAL* 3.6 51.3 + - + +
52B ILE* 4.1 13.6 - - + +
208B ALA* 3.6 25.8 - - + -
388B ILE* 3.9 33.7 - - + +
392B GLU* 2.8 14.5 + - + +
393B ALA* 3.3 13.5 - - - +
394B VAL 3.1 0.2 - - - -
395B ALA* 1.3 76.0 - - - +
397B GLY* 1.3 57.0 + - - +
399B ALA* 3.1 5.4 + - - +
400B VAL* 2.9 36.6 + - + +
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Residues in contact with GLY 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 4.8 0.2 - - - -
204B ALA* 3.2 28.9 - - - -
207B ILE* 4.0 6.8 - - - +
208B ALA* 3.6 12.0 - - - +
393B ALA 3.0 11.1 + - - -
394B VAL 3.7 1.3 - - - -
396B TYR* 1.3 73.6 - - - +
398B ALA* 1.3 65.4 + - - +
400B VAL* 3.2 5.1 + - - +
401B GLN* 3.2 25.4 + - - +
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Residues in contact with ALA 398 (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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32B GLY* 3.4 26.0 - - - -
33B ILE 3.9 3.4 - - - +
169B VAL* 3.9 22.8 - - + +
171B THR* 4.0 14.6 - - + -
199B ILE* 4.3 5.2 - - - -
204B ALA* 4.1 2.2 - - - +
394B VAL 3.0 13.5 + - - +
395B ALA* 3.5 8.1 - - - +
397B GLY* 1.3 74.1 - - - +
399B ALA* 1.3 57.5 + - - +
401B GLN* 3.2 5.1 + - - +
402B ALA* 2.9 27.7 + - - +
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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
----------------------------------------------------------
32B GLY* 3.8 4.2 - - - +
43B GLY* 3.7 27.1 - - - -
44B VAL* 3.9 4.3 - - - +
45B PHE* 3.9 6.8 + - - +
50B VAL* 3.7 21.1 - - + -
395B ALA 2.9 14.1 + - - +
396B TYR 3.1 10.0 + - - +
398B ALA* 1.3 73.8 - - - +
400B VAL* 1.3 59.5 + - - +
402B ALA* 3.2 8.7 + - - +
403B GLY* 2.8 27.4 + - - -
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 5.8 7.6 - - - +
45B PHE* 4.7 10.9 - - + -
50B VAL* 3.7 18.1 - - + +
207B ILE* 3.8 23.3 - - + +
208B ALA* 4.7 3.1 - - - -
212B ASP* 6.0 0.4 - - - +
213B LYS* 6.5 0.9 - - - -
396B TYR* 2.9 33.0 + - + +
397B GLY* 3.2 11.2 + - - +
399B ALA* 1.3 75.4 - - - +
401B GLN* 1.3 63.7 + - + +
403B GLY* 3.2 10.2 + - - -
404B VAL* 3.4 18.4 + - + +
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Residues in contact with GLN 401 (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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169B VAL* 4.5 8.7 - - + +
197B ARG* 3.3 29.9 + - - +
199B ILE* 3.4 37.4 - - + +
207B ILE* 3.4 29.5 - - + +
397B GLY 3.2 13.7 + - - +
398B ALA 3.7 6.3 - - - +
400B VAL* 1.3 76.7 - - + +
402B ALA* 1.3 63.1 + - - +
404B VAL* 3.2 10.5 + - - +
405B LEU* 3.0 27.3 + - - +
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Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.4 43.7 - - + +
31B VAL 3.8 12.6 - - - +
32B GLY 4.0 1.1 - - - +
43B GLY 5.3 0.2 - - - +
45B PHE 5.8 1.1 - - - +
169B VAL* 4.0 5.8 - - + +
398B ALA 2.9 18.1 + - - +
399B ALA* 3.5 6.5 - - - +
401B GLN* 1.3 74.9 - - - +
403B GLY* 1.3 55.1 + - - +
405B LEU* 3.3 2.2 + - - -
406B SER* 2.7 38.9 + - - -
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Residues in contact with GLY 403 (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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47A ASN* 5.7 2.8 - - - -
48A GLY* 5.7 2.0 - - - -
45B PHE* 3.6 33.6 - - - +
399B ALA 2.8 10.5 + - - -
400B VAL 3.6 4.3 - - - -
401B GLN 3.1 0.8 - - - -
402B ALA* 1.3 76.2 - - - +
404B VAL* 1.3 64.1 + - - +
406B SER* 3.0 23.8 + - - -
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 3.5 50.7 - - + +
48A GLY* 4.9 2.6 - - - +
197B ARG* 5.8 7.2 - - - +
400B VAL* 3.4 16.9 + - + +
401B GLN* 3.2 11.3 + - - +
403B GLY* 1.3 75.4 - - - +
405B LEU* 1.3 68.0 + - + +
406B SER 3.9 4.9 - - - -
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Residues in contact with LEU 405 (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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27B VAL* 4.1 12.5 - - - +
30B VAL* 4.2 11.7 - - + -
169B VAL* 3.7 26.7 - - + -
196B MET* 4.0 30.4 - - + +
197B ARG* 3.6 47.3 - - + +
401B GLN 3.0 20.1 + - - +
402B ALA* 3.8 4.0 - - - +
404B VAL* 1.3 78.1 - - + +
406B SER* 1.3 60.4 + - - +
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Residues in contact with SER 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 4.7 1.2 - - - +
28B GLY 3.7 20.4 - - - +
29B THR* 3.8 6.8 - - - +
30B VAL* 2.8 29.0 + - - +
45B PHE 6.0 2.0 - - - -
402B ALA 2.7 25.6 + - - -
403B GLY* 3.0 16.0 + - - -
404B VAL 3.9 4.3 - - - -
405B LEU* 1.3 81.5 - - - +
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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
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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