Contacts of the strand formed by residues 200 - 210 (chain A) in PDB entry 1U5Y
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 ASN 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.6 5.4 - - - +
162A PHE* 2.9 40.3 + - - +
189A ARG* 4.5 13.8 - - + -
190A SER 4.9 4.2 - - - +
191A MET* 4.4 15.9 - - - +
192A PRO* 3.6 17.5 - - - +
197A ARG 3.6 2.2 + - - -
198A ALA* 4.1 1.4 - - - +
199A TYR* 1.3 86.5 - - - +
201A SER* 1.3 61.6 + - - +
188D ILE 3.5 4.5 - - - +
189D ARG* 3.5 12.8 + - - -
190D SER* 3.0 43.5 + - - -
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Residues in contact with SER 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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159A GLN* 4.0 26.7 + - - -
160A VAL 3.4 6.7 - - - -
161A LEU* 4.0 12.3 - - - +
189A ARG* 3.0 22.7 + - - -
200A ASN* 1.3 73.6 - - - +
202A CYS* 1.3 60.6 + - - +
203A TYR* 4.1 1.3 + - - +
233A GLY* 5.9 0.2 - - - -
187D CYS* 3.8 14.4 - - - -
188D ILE* 3.0 36.1 + - - +
203D TYR 5.1 0.9 + - - -
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Residues in contact with CYS 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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159A GLN* 3.1 2.2 - - - -
160A VAL 2.8 31.0 + - - -
162A PHE* 3.7 15.3 - - + -
170A GLY* 4.8 1.6 - - - -
171A GLN* 3.1 19.0 + - - +
187A CYS* 2.0 54.3 - - - -
188A ILE 3.7 3.8 - - - -
189A ARG* 3.6 30.5 - - + +
201A SER* 1.3 74.5 - - - +
203A TYR* 1.3 59.5 + - - +
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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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157A TYR* 3.4 35.3 - + + +
158A SER 3.3 11.7 - - - -
159A GLN* 3.7 27.4 - - + +
187A CYS* 3.5 8.6 - - - -
189A ARG* 4.2 7.0 + - - +
201A SER* 4.1 1.7 + - - +
202A CYS* 1.3 73.9 - - - +
204A SER* 1.3 62.4 + - - +
205A ALA* 3.7 13.7 - - + +
235A PHE* 4.4 0.7 - + - -
159B GLN* 4.4 0.5 - - - +
203B TYR* 3.5 43.7 + + + +
155D LEU* 5.6 1.4 - - - +
203D TYR* 3.5 33.4 + + + +
204D SER* 4.1 0.4 - - - -
205D ALA* 3.2 48.7 - - + +
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Residues in contact with SER 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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157A TYR* 3.5 0.7 - - - +
158A SER 2.9 31.5 + - - +
171A GLN* 4.5 0.6 - - - +
185A PHE* 3.1 30.9 - - - -
186A ARG 4.5 0.7 - - - -
187A CYS* 4.0 16.3 - - - -
202A CYS 4.2 0.4 - - - -
203A TYR* 1.3 79.4 - - - +
205A ALA* 1.3 69.1 + - - +
159B GLN* 2.7 28.1 + - - -
203B TYR* 4.2 3.1 - - - -
235B PHE* 3.6 9.0 - - - -
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Residues in contact with ALA 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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155A LEU* 4.5 9.2 - - + -
156A LEU 3.2 15.7 - - - +
157A TYR* 3.6 14.8 - - + -
185A PHE* 3.8 6.3 - - - -
203A TYR* 3.7 10.3 - - + +
204A SER* 1.3 81.8 + - - +
206A GLY* 1.3 58.8 + - - +
157B TYR* 4.0 1.0 - - - -
203B TYR* 3.2 29.4 + - - +
235B PHE* 3.2 24.8 - - - -
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Residues in contact with GLY 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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155A LEU* 3.6 3.9 - - - +
156A LEU 2.9 31.9 + - - +
185A PHE* 4.1 0.6 - - - -
205A ALA* 1.3 75.1 - - - +
207A VAL* 1.3 63.4 + - - -
208A PHE* 3.3 25.5 - - - -
110B HIS* 4.7 0.4 - - - -
157B TYR* 3.8 17.0 - - - -
235B PHE* 4.7 2.0 - - - -
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Residues in contact with VAL 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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153A ILE* 3.3 32.3 - - + -
154A TYR 3.4 4.5 - - - +
155A LEU* 4.2 10.8 - - + -
206A GLY* 1.3 74.3 - - - +
208A PHE* 1.3 72.9 + - - +
241A LEU* 3.7 15.7 - - + -
108B VAL* 4.3 10.5 - - + -
109B LEU 5.7 1.1 - - - +
110B HIS* 3.5 18.6 - - + -
133B LEU* 3.6 13.3 - - + +
157B TYR* 2.9 32.5 + - + +
238B PHE 5.4 0.4 - - - +
239B VAL* 3.7 20.2 - - + -
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Residues in contact with PHE 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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153A ILE* 3.6 0.8 - - - -
154A TYR 3.0 32.2 + - - +
156A LEU* 4.6 7.4 - - + -
175A ARG* 6.2 0.4 - - - +
182A GLU* 5.7 1.6 - - - -
184A LEU* 3.5 54.3 - - + -
185A PHE* 3.6 24.9 - + + -
206A GLY* 3.3 31.6 - - - -
207A VAL* 1.3 75.6 - - - +
209A HIS* 1.3 63.0 + - - +
210A LEU* 3.5 21.6 + - + +
110B HIS* 3.4 31.9 - + - -
133B LEU* 3.8 9.0 - - - -
235B PHE* 5.8 0.7 - + - -
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Residues in contact with HIS 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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151A THR* 4.1 19.3 - - + +
152A GLY* 3.5 12.6 - - - -
153A ILE* 3.8 24.0 - - + +
175A ARG* 3.6 19.8 + - - -
208A PHE* 1.3 74.3 - - - +
210A LEU* 1.3 63.8 + - - +
211A HIS* 3.4 43.9 + + - -
133B LEU* 3.9 23.0 - - + +
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Residues in contact with LEU 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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148A VAL* 3.9 29.8 - - + -
150A ASP 4.2 0.5 - - - +
151A THR* 3.3 3.5 - - - +
152A GLY 2.8 32.4 + - - -
154A TYR* 3.7 33.2 - - + -
156A LEU* 4.7 10.5 - - + -
175A ARG* 3.5 25.1 - - - +
184A LEU* 4.4 6.5 - - + -
208A PHE* 3.9 19.5 - - + +
209A HIS* 1.3 80.3 + - - +
211A HIS* 1.3 62.4 + - - +
214A ASP* 3.6 4.7 - - - +
216A ILE* 3.9 19.7 - - + -
238A PHE* 4.7 5.8 - - + -
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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