Contacts of the helix formed by residues 197 - 210 (chain B) in PDB entry 1JVN
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 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B TRP* 3.4 24.5 - - - -
142B ARG 4.3 0.4 - - - +
143B TYR* 3.5 15.7 - - - +
144B TYR 3.0 21.1 + - - -
193B HIS 2.6 22.8 + - - -
194B PRO* 3.1 3.6 + - - +
196B LYS* 1.3 77.7 - - - +
198B GLY* 1.3 64.6 + - - +
199B LYS 3.6 0.2 + - - -
200B ALA* 3.6 8.8 + - - +
201B GLY* 3.2 25.5 + - - -
548B ARG* 4.7 0.4 + - - -
550B ASP* 3.7 4.3 - - - +
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TRP* 4.3 0.8 - - - -
194B PRO 4.0 1.6 - - - +
196B LYS 3.4 0.4 + - - -
197B SER* 1.3 76.5 - - - +
199B LYS* 1.3 58.5 + - - -
201B GLY* 3.1 2.1 + - - -
202B LEU* 3.0 31.0 + - - +
287B TYR* 3.8 16.8 - - - -
324B PHE* 2.8 23.1 + - - +
548B ARG* 4.3 11.4 - - - -
550B ASP* 4.0 2.9 - - - -
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Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 6.4 1.3 - - - -
198B GLY* 1.3 68.9 - - - -
200B ALA* 1.3 61.7 + - - +
202B LEU* 3.0 16.8 + - + +
203B ASN* 2.9 60.4 + - - +
206B GLU* 5.6 2.5 - - - -
287B TYR* 4.1 4.4 + - - -
550B ASP* 2.8 15.0 + - - +
551B GLU 3.4 26.4 + - - +
552B GLU* 3.7 39.6 + - + +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS* 4.0 28.9 - - + +
142B ARG 3.9 18.4 - - - +
143B TYR* 3.7 14.5 + - + -
197B SER 3.7 8.3 - - - +
198B GLY 3.3 0.2 - - - -
199B LYS* 1.3 75.5 - - - +
201B GLY* 1.3 61.8 + - - +
203B ASN* 3.4 10.0 + - - +
204B VAL* 3.4 23.9 + - - +
550B ASP* 3.0 17.6 + - - +
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 4.7 1.3 - - - -
194B PRO* 2.9 41.5 - - - +
197B SER* 3.2 15.5 + - - -
198B GLY 3.1 5.3 + - - -
200B ALA* 1.3 77.8 - - - +
202B LEU* 1.3 63.2 + - - +
204B VAL* 3.2 5.8 + - - +
205B ILE* 3.2 19.8 + - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 3.7 40.4 - - + +
23B HIS* 3.8 19.1 - - + -
24B LEU* 3.7 14.3 - - + +
194B PRO 3.8 2.4 + - - +
195B GLU* 5.6 0.4 - - - -
198B GLY 3.0 17.7 + - - +
199B LYS* 3.0 20.8 + - + +
201B GLY* 1.3 76.0 - - - +
203B ASN* 1.3 57.2 + - - +
205B ILE* 3.3 7.2 + - + +
206B GLU* 2.9 30.6 + - - +
324B PHE* 4.0 18.4 - - + -
552B GLU* 3.7 33.4 - - - +
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Residues in contact with ASN 203 (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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136B GLY 6.1 0.9 - - - +
141B LYS* 4.8 14.6 - - - +
199B LYS* 2.9 48.3 + - - +
200B ALA* 3.5 15.1 - - - +
201B GLY 3.2 0.4 - - - -
202B LEU* 1.3 77.0 - - - +
204B VAL* 1.3 52.5 + - + +
206B GLU* 3.4 14.8 + - - +
207B ASN* 2.8 48.9 + - - +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B MET* 4.1 9.6 - - + -
135B PHE 4.0 12.9 - - - +
136B GLY 5.3 1.6 - - - +
137B LEU* 3.8 16.8 - - + +
143B TYR* 3.7 25.4 - - + +
188B PHE* 3.7 32.4 - - + -
190B THR* 4.4 7.6 - - + -
192B PHE* 4.5 2.5 - - + -
194B PRO* 4.3 7.0 - - + -
200B ALA 3.4 14.8 - - - +
201B GLY 3.2 8.2 + - - +
203B ASN* 1.3 74.0 - - + +
205B ILE* 1.3 59.3 + - - +
207B ASN* 3.2 3.8 + - - +
208B PHE* 3.0 26.9 + - - +
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Residues in contact with ILE 205 (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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17B LEU* 4.2 15.0 - - + -
20B ALA* 4.0 22.4 - - + -
21B ILE* 4.4 13.9 - - + -
24B LEU* 3.6 16.2 - - + -
46B ILE* 5.3 5.4 - - + -
80B MET* 4.3 10.3 - - + -
194B PRO* 3.7 29.6 - - + +
195B GLU* 4.0 13.5 - - - +
201B GLY 3.2 11.5 + - - +
202B LEU* 3.6 8.5 - - - +
204B VAL* 1.3 74.5 - - - +
206B GLU* 1.3 57.5 + - - +
208B PHE* 3.2 7.5 + - - +
209B LEU* 3.0 41.0 + - + +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.6 33.2 - - + +
26B TYR* 5.6 1.1 - - + -
199B LYS* 5.6 2.3 - - - -
202B LEU 2.9 16.1 + - - +
203B ASN* 3.6 17.8 - - - +
205B ILE* 1.3 76.2 - - - +
207B ASN* 1.3 59.0 + - - +
209B LEU* 3.4 4.1 + - - +
210B LYS* 2.7 69.9 + - + +
212B GLN* 5.0 5.8 - - - +
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Residues in contact with ASN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 3.1 33.5 + - - +
136B GLY* 3.6 13.9 - - - -
203B ASN* 2.8 34.2 + - - +
204B VAL* 3.2 2.6 + - - +
206B GLU* 1.3 78.4 - - - +
208B PHE* 1.3 58.4 + - - +
211B GLN 3.1 4.0 + - - -
212B GLN* 2.9 65.2 + - - +
214B PRO* 3.3 20.8 - - - +
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Residues in contact with PHE 208 (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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44B ARG* 4.0 7.6 + - + -
45B LEU 3.8 10.3 - - - -
46B ILE* 4.1 11.0 - - + -
78B PRO* 3.7 12.6 - - + -
79B ILE* 3.4 32.5 - - - -
80B MET* 3.4 46.9 - - + -
135B PHE* 3.7 8.7 - + - -
186B ASN 4.9 0.9 - - - -
188B PHE* 3.8 26.0 - + + -
204B VAL 3.0 11.7 + - - +
205B ILE* 3.5 7.0 - - + +
206B GLU 3.2 0.2 - - - -
207B ASN* 1.3 76.1 - - - +
209B LEU* 1.3 79.1 + - + +
211B GLN* 2.9 50.8 + - - +
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Residues in contact with LEU 209 (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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2B PRO* 5.2 1.6 - - - +
4B VAL* 3.5 35.2 - - + -
21B ILE* 4.2 10.1 - - + -
24B LEU* 4.4 7.0 - - + -
26B TYR* 3.6 51.3 + - + +
44B ARG* 2.6 39.9 + - + +
46B ILE* 4.5 3.4 - - + -
205B ILE* 3.0 35.5 + - + +
206B GLU 3.4 3.8 + - - +
208B PHE* 1.3 91.1 - - + +
210B LYS* 1.3 56.5 + - - +
211B GLN 3.3 0.2 - - - -
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU 5.4 3.4 + - - -
26B TYR* 3.1 27.8 - - + +
44B ARG* 4.7 3.1 - - - +
206B GLU* 2.7 54.3 + - + +
209B LEU* 1.3 73.6 - - - +
211B GLN* 1.3 72.2 + - - +
212B GLN* 3.3 31.2 + - - +
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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