Contacts of the helix formed by residues 199 - 207 (chain B) in PDB entry 4UT2
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 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B ASP* 4.0 13.5 - - - -
196B PRO* 5.6 0.4 - - - -
198B GLN* 1.3 77.4 - - - +
200B LEU* 1.3 65.9 + - - -
201B LEU 3.4 2.5 - - - -
202B CYS* 3.2 3.0 + - - +
203B ASP* 3.0 33.8 + - - +
225B PHE* 6.2 1.2 - - - -
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Residues in contact with LEU 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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177B SER* 3.6 30.7 - - - +
179B ASP* 4.1 11.8 + - + -
180B LEU* 3.8 24.9 - - + +
185B GLN* 3.8 48.0 - - + +
186B ILE* 4.2 5.6 - - + +
189B ILE* 4.3 11.7 - - + -
199B GLY* 1.3 70.7 - - - -
201B LEU* 1.3 64.5 + - - +
203B ASP* 3.3 2.3 + - - +
204B LEU* 3.0 44.5 + - + +
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Residues in contact with LEU 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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122B ARG* 4.6 3.4 - - - +
161B ILE* 3.5 42.6 - - + -
189B ILE* 4.4 21.9 - - + +
193B THR* 3.8 29.2 - - + -
194B ASP 4.0 3.1 - - - +
195B VAL* 4.1 12.1 - - + -
196B PRO* 3.7 29.3 - - + +
199B GLY 3.4 0.6 - - - -
200B LEU* 1.3 78.4 - - - +
202B CYS* 1.3 63.9 + - - +
204B LEU* 3.4 3.6 + - - +
205B LEU* 3.4 29.3 + - + +
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Residues in contact with CYS 202 (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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195B VAL* 4.1 10.5 - - - -
196B PRO* 3.4 21.8 - - - +
197B ASP* 3.6 12.6 - - - -
198B GLN* 3.8 13.0 - - - +
199B GLY 3.2 10.8 + - - +
201B LEU* 1.3 78.8 - - - +
203B ASP* 1.3 63.0 + - - +
205B LEU 3.1 3.6 + - - -
206B TRP* 3.0 36.2 + - - +
223B VAL* 3.5 32.8 - - - -
224B SER* 4.4 8.3 - - - -
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Residues in contact with ASP 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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175B GLY 3.6 2.3 + - - +
176B LEU 3.7 3.4 - - - +
177B SER* 2.4 42.5 + - - +
178B PRO* 3.3 16.1 - - - +
179B ASP* 4.7 2.3 - - - +
198B GLN* 5.9 0.2 - - - -
199B GLY* 3.0 22.1 + - - +
200B LEU 3.3 1.5 + - - +
202B CYS* 1.3 78.0 - - - +
204B LEU* 1.3 61.9 + - - +
207B SER* 3.1 31.0 + - - -
224B SER* 2.8 31.5 + - - +
225B PHE* 3.5 16.5 - - - -
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 3.6 24.2 - - + -
162B ALA* 5.5 0.4 - - + -
170B PHE* 4.3 23.8 - - + -
172B CYS* 3.8 15.0 - - + +
173B HIS 3.8 1.7 + - - -
174B GLY* 2.9 21.8 + - - -
175B GLY 3.4 19.9 + - - +
176B LEU* 4.9 1.3 - - - -
177B SER* 5.1 1.8 - - - +
180B LEU* 4.3 14.8 - - + -
186B ILE* 3.9 23.6 - - + -
189B ILE* 4.5 4.7 - - + -
200B LEU* 3.0 34.1 + - + +
201B LEU* 3.7 5.6 - - - +
202B CYS 3.3 0.2 - - - -
203B ASP* 1.3 77.4 - - - +
205B LEU* 1.3 66.7 + - + +
206B TRP 3.6 0.2 - - - -
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Residues in contact with LEU 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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122B ARG* 3.5 34.3 - - + +
123B GLY* 3.6 23.3 - - - +
124B ASN* 3.4 23.6 - - - +
161B ILE* 4.1 20.6 - - + +
173B HIS* 3.5 16.2 - - + -
174B GLY* 3.9 8.3 - - - +
195B VAL* 3.7 28.7 - - + -
201B LEU* 3.4 19.3 + - + +
202B CYS 3.1 5.0 + - - +
204B LEU* 1.3 91.6 - - + +
206B TRP* 1.3 67.1 + - + +
248B HIS* 3.6 1.9 - - - -
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Residues in contact with TRP 206 (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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124B ASN* 3.4 41.3 + - + +
130B ILE* 3.7 32.3 - - + -
195B VAL* 4.3 13.9 - - + +
196B PRO 5.5 0.2 + - - -
202B CYS* 3.0 39.3 + - - +
203B ASP 3.3 0.2 + - - -
204B LEU 3.6 0.2 - - - -
205B LEU* 1.3 85.5 - - + +
207B SER* 1.3 65.9 + - - +
208B ASP* 3.8 0.9 - - - +
219B ASN* 4.0 2.3 + - - -
221B ARG* 3.7 41.6 + - + -
223B VAL* 3.3 32.5 - - + +
224B SER* 3.6 17.6 - - - -
248B HIS* 2.9 19.2 + + - -
501B PO4 5.4 2.5 - - - -
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Residues in contact with SER 207 (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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174B GLY 3.3 12.5 - - - -
175B GLY* 3.1 20.7 - - - +
176B LEU 3.0 25.4 + - - -
203B ASP* 3.1 7.7 + - - -
206B TRP* 1.3 81.1 - - - +
208B ASP* 1.3 59.4 + - - +
216B TRP* 5.2 1.6 - - - -
219B ASN* 4.2 0.2 - - - +
224B SER* 3.4 12.9 + - - -
225B PHE* 3.3 20.9 - - - -
227B PHE* 3.4 8.7 - - - -
246B ARG* 3.2 15.2 + - - -
248B HIS* 3.5 0.5 - - - -
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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