Contacts of the strand formed by residues 198 - 207 (chain A) in PDB entry 3UF4
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 ASP 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.9 26.4 - - + +
190A ARG* 3.3 27.7 + - - +
191A ASP 3.6 8.9 - - - +
192A TRP* 3.7 20.3 + - - +
197A GLY* 1.3 71.2 + - - -
199A HIS* 1.3 60.5 + - - +
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Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.3 7.2 - - - -
190A ARG* 3.5 6.6 - - - +
191A ASP* 2.8 36.7 + - + +
192A TRP 3.7 12.3 - - - -
193A ASP* 3.3 40.5 + - - -
196A LYS* 3.6 31.7 - - + +
197A GLY 2.9 18.8 + - - -
198A ASP* 1.3 75.7 - - - +
200A VAL* 1.3 68.8 + - - +
201A LYS* 2.9 40.4 + - + +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU* 4.0 25.8 + - + +
163A LEU* 3.8 34.5 - - + -
164A LEU* 4.0 18.3 - - + +
188A SER* 3.9 0.4 - - - -
189A ILE 3.3 18.6 - - - +
190A ARG* 4.3 3.1 - - - -
199A HIS* 1.3 86.5 - - - +
201A LYS* 1.3 69.8 + - - +
202A HIS* 3.5 35.2 + - + -
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU 3.6 1.2 - - - +
188A SER* 3.4 2.9 - - - -
189A ILE* 2.9 34.1 + - - +
191A ASP* 2.7 26.4 + - + +
193A ASP* 4.1 8.1 + - - +
196A LYS* 4.1 14.6 - - - +
199A HIS* 2.9 30.7 + - + +
200A VAL* 1.3 76.4 - - - +
202A HIS* 1.3 59.7 - - - +
203A TYR* 3.6 32.9 - - + +
239A CYS* 3.6 19.4 - - + +
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Residues in contact with HIS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG* 3.3 53.7 - - + +
159A ALA* 4.8 1.1 - - + -
160A GLU* 2.8 34.1 + - + +
176A ARG* 3.1 19.0 + - - +
186A SER* 5.5 2.2 - - - -
187A LEU 3.4 4.5 - - - +
188A SER* 2.9 24.8 + - - -
200A VAL* 3.5 27.0 + - + +
201A LYS* 1.3 74.6 - - - +
203A TYR* 1.3 65.3 + - - +
204A LYS 4.2 0.6 + - - -
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A SER* 3.4 2.9 - - - -
187A LEU* 2.8 45.9 + - + +
189A ILE* 3.6 28.3 - - + -
201A LYS* 3.6 29.3 - - + +
202A HIS* 1.3 75.5 - - - +
204A LYS* 1.3 64.0 + - - +
205A ILE* 3.5 0.7 + - - +
215A ILE* 4.1 30.5 - - + -
237A GLY 5.1 2.2 + - - -
238A LEU* 3.7 29.2 - - + -
239A CYS* 3.0 33.8 + - - +
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Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A SER* 4.3 5.8 - - - +
180A THR* 3.6 17.8 + - - +
181A THR* 2.6 38.3 + - - +
184A ALA* 4.3 3.6 - - + -
185A TYR 3.6 9.0 - - - +
186A SER* 4.5 5.2 - - - +
202A HIS 4.2 1.2 + - - -
203A TYR* 1.3 71.5 - - - +
205A ILE* 1.3 63.4 + - - +
206A ARG* 3.9 41.6 + - + +
214A TYR 4.0 2.4 - - - +
215A ILE* 3.8 18.2 - - - +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.8 29.6 - - + -
184A ALA* 3.4 7.8 - - - +
185A TYR* 2.6 47.5 + - + +
187A LEU* 3.8 21.5 - - + +
203A TYR 4.0 4.9 - - - +
204A LYS* 1.3 72.1 - - - +
206A ARG* 1.3 60.4 + - - +
213A TYR* 3.8 32.3 - - + -
214A TYR 3.5 4.9 - - - +
215A ILE* 3.7 19.3 - - + -
224A LEU* 3.9 15.9 - - + -
227A LEU* 4.0 19.3 - - + -
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Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 6.1 2.7 - - + -
184A ALA* 4.6 5.8 - - + -
204A LYS* 3.9 38.7 + - + +
205A ILE* 1.3 76.2 - - - +
207A LYS* 1.3 62.6 + - - +
213A TYR* 3.3 7.1 - - - -
214A TYR* 3.0 77.2 + - + +
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLY 4.6 10.2 + - - +
184A ALA* 5.6 0.8 - - - +
206A ARG* 1.3 78.1 - - - +
208A LEU* 1.3 74.8 + - - +
209A ASP* 4.0 2.9 + - - +
211A GLY 4.0 12.1 - - - -
212A GLY* 3.5 17.3 - - - +
213A TYR* 3.7 44.9 + - + +
214A TYR* 4.3 3.0 - - - -
222A GLU 5.8 0.9 - - - -
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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