Contacts of the strand formed by residues 199 - 210 (chain A) in PDB entry 1UXU
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 TYR 199 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TYR* 6.0 0.7 - - - +
154A ASN* 4.2 21.1 - - + -
188A ASN 4.0 0.9 - - - +
189A VAL* 3.6 2.0 - - - +
190A ILE* 2.9 48.6 + - + +
192A TYR* 4.2 28.9 - + - -
196A SER* 4.2 5.9 + - - -
197A GLU* 3.5 26.9 + - + +
198A PRO* 1.3 77.7 - - - +
200A PRO* 1.3 64.9 - - - +
201A ASP* 5.1 0.5 - - - +
1213A MLK 3.8 82.2 - - + +
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Residues in contact with PRO 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.9 17.6 + - - +
149A GLY* 4.3 4.0 - - - -
150A SER 5.0 0.7 + - - -
153A TYR 5.3 2.2 - - - +
154A ASN* 4.4 2.2 - - - -
155A GLY* 3.5 25.1 - - - +
158A VAL 4.2 8.3 - - - +
159A ASP* 4.1 15.0 - - - +
160A ILE* 4.0 18.6 - - + +
187A LYS* 4.3 2.9 - - - -
188A ASN 3.2 9.4 - - - +
189A VAL* 4.1 16.2 - - + -
198A PRO 3.5 10.1 - - - +
199A TYR* 1.3 88.1 - - - +
201A ASP* 1.3 63.1 + - - +
1213A MLK 5.1 0.4 - - - -
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Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 4.0 10.1 - - + -
147A THR* 3.6 20.4 - - + +
148A PHE 3.2 15.0 - - - +
160A ILE* 4.2 4.9 - - - -
187A LYS* 3.4 9.0 - - - +
188A ASN* 2.8 57.3 + - - +
199A TYR 5.1 0.5 - - - +
200A PRO* 1.3 74.8 - - - +
202A VAL* 1.3 63.6 + - - +
203A THR* 3.0 20.8 + - - -
1213A MLK 3.6 20.5 - - + -
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Residues in contact with VAL 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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35A LEU* 3.8 30.3 - - + -
146A LEU 3.7 1.6 - - - +
147A THR* 3.5 0.9 - - - -
148A PHE* 2.8 36.3 + - + +
160A ILE* 3.8 25.3 - - + +
161A PHE 4.2 2.2 - - - +
162A ASN* 3.7 37.2 - - - +
186A VAL 3.3 7.2 - - - +
187A LYS* 4.3 6.7 - - + -
201A ASP* 1.3 80.9 - - - +
203A THR* 1.3 59.4 + - - +
204A PHE* 4.0 15.9 - - + -
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Residues in contact with THR 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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145A ASN* 3.9 15.3 - - + +
146A LEU 3.3 3.6 - - - +
147A THR* 2.8 27.1 + - - +
184A PRO 3.8 0.7 - - - +
185A ALA* 3.4 3.2 - - - -
186A VAL* 2.9 35.6 + - - +
188A ASN* 3.6 13.3 + - - -
201A ASP* 3.0 19.8 + - - -
202A VAL* 1.3 71.4 - - - +
204A PHE* 1.3 67.8 + - - +
205A THR* 4.0 0.7 + - - +
2215A NAG 3.5 32.2 + - - +
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Residues in contact with PHE 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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35A LEU* 4.3 9.2 - - + -
36A GLN* 5.2 0.2 - - - -
37A ILE* 3.4 39.9 - - + -
144A CYS 3.6 0.3 - - - +
145A ASN* 3.4 2.8 - - - -
146A LEU* 2.8 47.3 + - + +
148A PHE* 3.9 8.3 - + - -
162A ASN* 3.5 16.6 - - - -
164A LEU* 5.7 0.7 - - + -
166A SER 4.1 4.0 - - - -
167A GLY* 3.6 31.6 - - - -
183A MET* 3.9 24.7 - - + -
184A PRO 3.5 2.9 - - - -
185A ALA* 3.5 23.3 - - + -
202A VAL* 4.0 21.3 - - + -
203A THR* 1.3 74.7 - - - +
205A THR* 1.3 61.1 + - - +
206A LEU 3.4 2.8 + - - -
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Residues in contact with THR 205 (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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143A GLN* 3.6 34.1 - - + +
145A ASN* 2.8 23.8 + - - +
183A MET* 4.1 2.2 - - - -
184A PRO* 3.0 45.1 + - + +
186A VAL* 6.1 0.5 - - - +
203A THR* 4.0 1.6 + - - +
204A PHE* 1.3 72.1 - - - +
206A LEU* 1.3 60.4 + - - +
207A LEU* 3.3 8.0 + - + +
2215A NAG 3.5 22.3 + - - -
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Residues in contact with LEU 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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39A LEU* 4.1 24.9 - - + -
42A ILE* 5.2 1.8 - - + -
52A LEU* 3.7 30.3 - - + -
142A GLN 3.5 3.3 - - - +
143A GLN* 3.8 0.7 - - - -
144A CYS* 2.8 45.9 + - + +
146A LEU* 5.0 5.4 - - + -
180A VAL* 3.8 29.4 - - + -
182A GLY 3.6 5.2 - - - +
183A MET* 3.9 30.7 - - + +
204A PHE 3.4 2.7 + - - +
205A THR* 1.3 71.6 - - - +
207A LEU* 1.3 56.0 + - - +
208A LEU* 3.7 24.9 + - + -
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Residues in contact with LEU 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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133A ASP* 4.4 7.2 - - - +
136A TYR* 6.1 0.9 - - + -
137A PHE 3.9 17.7 - - - +
138A PRO* 4.1 6.3 - - + -
141A ASN* 3.7 24.5 - - + +
142A GLN 3.6 14.1 - - - +
143A GLN* 4.0 22.0 - - + +
180A VAL* 3.8 2.6 - - - -
181A HIS* 2.8 54.9 + - + +
182A GLY* 2.9 22.8 + - - +
184A PRO* 5.9 1.1 - - + -
205A THR* 3.3 8.4 + - + +
206A LEU* 1.3 71.7 - - - +
208A LEU* 1.3 57.2 + - - +
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Residues in contact with LEU 208 (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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42A ILE* 3.8 32.8 - - + -
45A MET* 4.2 21.3 - - + -
52A LEU* 4.3 10.1 - - + -
141A ASN* 3.0 10.2 - - - +
142A GLN* 2.9 38.4 + - + +
144A CYS* 4.2 18.4 - - - -
178A TRP* 3.8 19.5 - - + -
179A GLU 3.4 5.4 - - - +
180A VAL* 4.0 9.6 - - + -
181A HIS* 5.1 0.2 - - - -
206A LEU* 3.7 33.0 - - + +
207A LEU* 1.3 77.1 - - - +
209A LYS* 1.3 58.3 + - - +
210A ARG 4.1 0.2 + - - -
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Residues in contact with LYS 209 (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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138A PRO* 3.7 45.3 - - + +
140A ASP* 3.6 12.1 - - + +
141A ASN* 4.2 0.9 - - - -
178A TRP* 3.5 3.7 - - - -
179A GLU* 2.8 73.4 + - + +
181A HIS* 4.6 7.2 - - + -
207A LEU 4.1 1.2 + - - -
208A LEU* 1.3 72.2 - - - +
210A ARG* 1.3 76.2 + - - +
211A ARG* 3.4 0.6 + - - +
212A SER 6.0 0.7 - - - +
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Residues in contact with ARG 210 (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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47A GLU* 2.8 43.6 + - - -
132A VAL* 5.7 5.5 - - - +
140A ASP* 2.9 52.7 + - - +
141A ASN 5.5 2.6 + - - -
142A GLN* 4.8 1.6 - - - +
177A GLU* 3.8 4.3 - - - +
178A TRP* 3.4 33.9 - - + -
209A LYS* 1.3 90.1 - - - +
211A ARG* 1.3 75.4 + - - +
212A SER* 3.6 3.0 + - - +
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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