Contacts of the helix formed by residues 192 - 201 (chain B) in PDB entry 1F4J
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 SER 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B PHE* 3.0 23.7 + - - +
155B ILE* 5.5 1.3 - - - -
186B TRP* 3.4 45.7 + - - +
189B ARG* 2.9 20.9 + - - -
190B PRO* 2.8 1.4 - - - +
191B GLU* 1.3 77.8 - - - +
193B LEU* 1.3 59.2 + - - +
194B HIS 3.4 0.6 + - - -
195B GLN* 3.5 3.5 + - - -
196B VAL* 2.9 37.7 + - - +
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Residues in contact with LEU 193 (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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190B PRO* 2.8 36.4 + - + +
191B GLU 3.0 0.6 - - - -
192B SER* 1.3 79.4 + - - +
194B HIS* 1.3 64.7 + - - +
196B VAL* 3.3 5.3 + - + +
197B SER* 3.0 28.8 + - - +
439B ASN 3.5 21.3 - - - +
440B VAL* 3.7 18.8 - - + -
443B VAL* 4.1 7.9 - - + -
481B ASN* 3.8 25.4 - - + +
482B PHE* 3.8 35.0 - - + -
484B GLU* 5.6 0.2 - - + -
485B VAL* 3.8 11.4 - - + -
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Residues in contact with HIS 194 (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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152B ILE* 3.3 24.9 - - + +
191B GLU 4.1 6.5 + - - +
192B SER 3.4 0.8 - - - -
193B LEU* 1.3 81.4 - - - +
195B GLN* 1.3 61.1 - - - +
197B SER* 3.3 3.6 + - - -
198B PHE* 3.2 16.1 + - + +
300B THR* 2.7 29.7 + - - +
301B LYS* 5.4 1.0 - - - -
302B VAL* 4.3 9.6 - - + +
439B ASN 4.9 0.2 + - - -
442B GLN* 3.1 45.5 + - + +
443B VAL* 3.6 30.3 - - + +
446B PHE* 4.5 17.9 - + + +
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Residues in contact with GLN 195 (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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129B PRO* 4.3 10.9 - - - +
150B THR* 2.7 39.7 + - - +
152B ILE* 3.2 16.9 - - + +
153B PHE* 3.2 34.9 + - + +
154B PHE* 3.4 33.7 - - + +
192B SER 3.5 2.0 + - - -
193B LEU 3.4 0.4 - - - -
194B HIS* 1.3 74.6 - - - +
196B VAL* 1.3 61.2 + - - +
197B SER 3.1 1.8 - - - -
198B PHE* 3.7 8.1 - - - +
199B LEU* 2.8 43.2 + - - +
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PHE* 3.8 9.6 - - + -
183B TRP* 4.2 15.7 - - + -
186B TRP* 3.6 37.7 - - + -
192B SER* 2.9 34.2 + - - +
193B LEU* 3.3 6.0 + - + +
195B GLN* 1.3 77.3 - - - +
197B SER* 1.3 61.1 + - - +
199B LEU* 3.6 2.4 + - - -
200B PHE* 3.0 42.4 + - + +
459B LEU* 4.8 0.2 - - - +
463B ILE* 4.6 1.6 - - + -
482B PHE* 4.3 19.5 - - + -
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Residues in contact with SER 197 (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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193B LEU* 3.0 13.1 + - - +
194B HIS 3.4 10.3 - - - -
196B VAL* 1.3 77.8 - - - +
198B PHE* 1.3 65.9 + - - +
200B PHE 3.4 0.7 + - - -
201B SER* 3.2 22.3 + - - -
443B VAL* 3.7 8.1 - - - +
446B PHE* 3.9 24.7 - - - -
459B LEU* 3.6 11.0 - - - +
482B PHE* 5.0 1.0 - - - -
489B TYR* 2.7 36.7 + - - -
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Residues in contact with PHE 198 (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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149B ASN* 3.7 23.6 - - - -
150B THR* 3.7 30.1 - - - +
151B PRO* 4.4 13.5 - - + -
152B ILE* 4.7 5.6 - - + -
194B HIS* 3.2 9.7 + - + +
195B GLN* 3.7 18.4 - - - +
197B SER* 1.3 79.6 - - - +
199B LEU* 1.3 64.6 + - - +
201B SER* 2.9 25.1 + - - +
203B ARG* 3.7 51.1 - - + -
204B GLY 4.2 3.6 + - - -
215B TYR* 5.2 1.1 - - - -
446B PHE* 4.3 23.1 - + + -
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Residues in contact with LEU 199 (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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127B ARG* 3.1 23.9 + - + +
128B ASP* 3.5 45.3 - - - +
129B PRO* 3.8 11.4 - - + -
154B PHE* 3.4 24.2 - - + -
168B GLN* 5.6 3.1 - - - +
186B TRP* 3.9 19.7 - - + -
195B GLN* 2.8 26.5 + - - +
196B VAL 3.9 3.8 - - - +
197B SER 3.2 0.2 - - - -
198B PHE* 1.3 79.8 - - - +
200B PHE* 1.3 66.4 + - + +
201B SER 3.4 0.2 - - - -
204B GLY* 3.2 15.1 - - - -
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Residues in contact with PHE 200 (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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127B ARG* 3.6 27.1 - - - +
183B TRP* 3.8 19.7 - + - -
186B TRP* 3.8 28.0 - + - -
196B VAL* 3.0 35.1 + - + +
197B SER 3.4 0.4 + - - -
198B PHE 3.3 0.2 - - - -
199B LEU* 1.3 85.0 - - + +
201B SER* 1.3 61.5 + - - +
459B LEU* 3.6 25.9 - - + -
462B ASN* 2.8 60.8 + - + +
463B ILE* 3.6 14.1 - - + -
466B HIS* 4.1 19.7 - + + -
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Residues in contact with SER 201 (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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127B ARG* 3.7 4.5 + - - -
197B SER 3.2 11.8 + - - -
198B PHE* 2.9 20.7 + - - -
200B PHE* 1.3 84.1 - - - +
202B ASP* 1.3 67.2 + - - +
203B ARG* 3.2 15.6 + - - +
204B GLY* 2.9 13.0 + - - -
446B PHE* 4.4 16.4 - - - -
451B LEU* 4.7 13.2 - - - -
455B GLN* 5.5 3.1 - - - -
458B ARG* 6.4 0.4 - - - -
459B LEU* 4.6 10.3 - - - +
462B ASN* 4.6 2.3 + - - -
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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
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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