Contacts of the strand formed by residues 180 - 189 (chain B) in PDB entry 3UP1
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 MET 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLN* 3.7 7.4 - - - +
152B GLU* 2.9 50.6 + - + +
179B ALA* 1.3 71.0 - - - +
181B TYR* 1.3 61.1 + - - +
205B TYR* 3.8 25.8 - - + +
206B PHE* 3.4 8.1 - - - +
207B ARG* 3.6 52.7 - - - +
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Residues in contact with TYR 181 (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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149B TYR* 4.2 18.6 - + + -
150B ARG* 3.4 19.7 - - - -
151B GLN* 3.7 25.0 + - + -
152B GLU* 4.4 3.6 - - - -
155B GLU* 4.8 3.2 + - - -
174B LYS 4.9 0.3 + - - -
175B LEU* 3.5 26.8 - - + +
176B GLN* 2.8 47.0 + - - +
179B ALA* 3.7 21.1 - - + -
180B MET* 1.3 75.9 - - - +
182B GLU* 1.3 61.1 + - - +
204B TYR 3.6 0.7 - - - +
205B TYR* 3.1 8.3 - - - +
206B PHE* 2.7 58.9 + + + +
208B THR* 3.9 9.6 - - + -
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Residues in contact with GLU 182 (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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149B TYR* 3.1 6.2 - - - +
150B ARG* 2.9 52.7 + - + +
152B GLU* 4.2 14.6 - - + +
158B TRP* 3.2 32.0 - - + -
181B TYR* 1.3 74.8 - - - +
183B ILE* 1.3 63.7 + - - +
184B LYS* 4.6 1.7 + - - +
203B SER* 2.7 28.8 + - - +
204B TYR 3.4 3.4 - - - -
205B TYR* 3.6 33.2 + - + -
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Residues in contact with ILE 183 (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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115B LEU* 3.6 8.0 - - + +
117B VAL* 4.4 7.2 - - + -
128B VAL* 3.8 31.0 - - + -
147B VAL* 3.6 27.4 - - + -
148B ALA 3.3 10.3 - - - +
149B TYR* 3.9 14.1 - - + -
170B LEU* 4.2 11.2 - - + -
182B GLU* 1.3 78.8 - - - +
184B LYS* 1.3 65.1 + - - +
203B SER* 3.3 2.7 - - - -
204B TYR* 2.7 62.1 + - + +
206B PHE* 4.1 22.2 - - + -
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Residues in contact with LYS 184 (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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115B LEU* 3.7 3.1 - - - -
146B ASP 4.0 0.2 - - - +
147B VAL* 3.5 3.1 - - - +
148B ALA* 2.7 42.0 + - + +
158B TRP* 3.7 41.0 - - + +
182B GLU* 4.6 1.6 + - - +
183B ILE* 1.3 76.7 - - - +
185B VAL* 1.3 63.1 + - - +
200B TRP* 3.5 55.9 - - + +
201B SER* 3.7 22.0 - - - +
203B SER* 4.0 18.2 - - - +
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Residues in contact with VAL 185 (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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112B PRO* 3.6 18.9 - - + +
115B LEU* 3.6 33.7 - - + -
130B PHE* 3.9 28.7 - - + -
145B HIS* 4.3 1.8 - - + -
146B ASP 3.3 12.1 - - - +
147B VAL* 3.8 24.9 - - + -
184B LYS* 1.3 81.4 - - - +
186B ARG* 1.3 70.9 + - - +
200B TRP* 3.5 3.3 - - - -
201B SER* 2.7 40.7 + - - +
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Residues in contact with ARG 186 (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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112B PRO* 3.7 4.3 - - - -
145B HIS* 3.3 4.9 - - - +
146B ASP* 2.7 62.5 + - + +
160B HIS* 4.6 6.5 - - - -
185B VAL* 1.3 74.3 - - - +
187B SER* 1.3 62.7 + - - +
197B TRP* 3.6 55.7 - - + +
198B SER* 3.6 20.8 + - - +
199B GLU 3.8 7.0 - - - +
200B TRP* 3.3 44.7 - - + +
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Residues in contact with SER 187 (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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109B PRO* 3.6 11.8 - - - +
110B GLU 4.7 1.9 + - - -
112B PRO* 3.3 13.9 - - - +
132B THR* 4.8 0.5 + - - +
143B LEU* 4.0 19.0 - - - +
144B MET 3.4 6.1 - - - -
145B HIS* 2.6 30.6 + - - -
186B ARG* 1.3 75.7 - - - +
188B ILE* 1.3 60.7 + - - +
197B TRP* 3.4 4.9 - - - -
198B SER* 2.6 43.9 + - - -
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Residues in contact with ILE 188 (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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109B PRO* 4.0 0.2 - - - -
143B LEU* 3.6 6.0 - - - -
144B MET* 3.0 44.0 + - + +
187B SER* 1.3 75.7 - - - +
189B PRO* 1.3 91.1 - - + +
190B ASP* 5.5 0.2 - - + -
195B GLY 4.1 14.8 - - - +
196B PHE* 3.7 9.6 - - - +
197B TRP* 3.5 53.6 - - + +
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Residues in contact with PRO 189 (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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107B VAL* 3.5 29.2 - - + +
109B PRO* 3.6 13.7 - - + -
142B VAL* 3.9 1.1 - - + +
143B LEU* 3.9 13.2 - - + -
188B ILE* 1.3 103.5 - - + +
190B ASP* 1.3 58.7 + - - +
193B PHE* 3.8 18.6 - - + +
194B LYS* 3.7 30.1 - - - +
195B GLY 4.1 1.7 + - - -
196B PHE 3.5 15.0 - - - +
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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