Contacts of the strand formed by residues 155 - 163 (chain B) in PDB entry 5UWS
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 SER 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A LEU* 3.2 26.1 - - - +
148B PRO* 4.2 8.7 - - - +
149B ASN* 4.4 8.1 + - - -
152B SER* 2.7 27.8 + - - +
153B ASP 5.2 1.2 - - - -
154B ARG* 1.3 75.5 - - - +
156B TRP* 1.3 82.2 + - - +
176B ILE 3.2 10.8 - - - -
177B ARG* 3.0 23.2 - - - +
184B ALA* 4.3 0.6 - - - +
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Residues in contact with TRP 156 (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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146B LEU* 4.0 34.1 - - + -
147B LYS 3.6 15.5 - - - -
148B PRO* 4.1 22.7 - - + -
155B SER* 1.3 88.5 - - - +
157B VAL* 1.3 63.2 + - - +
158B TYR* 4.4 1.9 + - - -
174B PHE 3.9 0.5 - - - +
175B ALA* 3.2 4.9 - - - +
176B ILE* 3.0 37.2 + - + +
178B PHE* 3.8 20.2 - + - -
184B ALA* 2.7 36.5 + - + +
185B ASP* 4.0 17.9 - - - -
187B PHE* 3.8 13.0 - + - -
188B LYS* 3.7 37.0 - - + +
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.6 22.7 - - + -
204A ALA* 4.2 7.0 - - + +
205A GLN* 4.3 11.4 - - + -
103B TRP* 4.0 15.0 - - + -
145B THR 3.5 0.9 - - - +
146B LEU* 3.6 0.6 - - - -
147B LYS* 2.6 48.1 + - - +
148B PRO 4.5 0.4 - - - +
149B ASN* 3.9 36.3 - - + +
156B TRP* 1.3 77.5 - - - +
158B TYR* 1.3 66.9 + - - +
173B THR* 4.2 4.0 - - + -
174B PHE 3.3 9.6 - - - +
175B ALA* 4.0 14.6 - - + -
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 4.1 10.1 - - - -
93B LEU* 5.6 2.7 - - + +
124B ILE* 3.8 11.1 - - - +
138B HIS* 3.1 33.4 + - - -
144B TYR* 4.3 24.5 - + + -
145B THR 3.1 31.4 - - - +
146B LEU* 3.4 22.9 - - + -
156B TRP 4.6 2.2 - - - -
157B VAL* 1.3 75.4 - - - +
159B ALA* 1.3 72.1 + - - +
160B CYS* 4.7 7.6 - - + -
173B THR* 4.6 0.7 - - - -
174B PHE* 2.9 52.7 + + + +
176B ILE* 4.7 16.7 - - + +
187B PHE* 5.5 2.3 - + - -
191B PHE* 4.4 12.8 - + - -
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Residues in contact with ALA 159 (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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197A TYR* 4.8 23.8 - - + +
201A LEU* 4.1 18.7 - - + +
144B TYR* 3.3 24.2 - - - +
145B THR 5.0 0.8 + - - +
158B TYR* 1.3 79.9 - - - +
160B CYS* 1.3 61.1 + - - +
161B THR* 5.5 2.0 - - + -
172B PHE 3.4 8.1 - - - +
173B THR* 4.2 10.8 - - - +
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Residues in contact with CYS 160 (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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197A TYR* 5.9 0.4 - - - -
138B HIS* 3.6 42.8 - - - -
144B TYR* 3.6 15.7 - - + -
158B TYR* 3.9 4.2 + - + -
159B ALA* 1.3 75.2 - - - +
161B THR* 1.3 62.0 + - - +
162B ALA 3.9 12.1 - - - -
163B ASP* 4.1 5.6 - - - -
171B ALA* 3.2 4.5 - - - +
172B PHE* 2.6 43.7 + - + +
174B PHE* 3.8 21.8 - - + -
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Residues in contact with THR 161 (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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187A VAL* 4.4 23.5 - - - +
197A TYR* 4.6 21.1 - - + -
143B GLU* 4.5 11.5 + - - +
144B TYR* 2.9 32.1 + - + -
159B ALA* 5.4 2.9 - - + +
160B CYS* 1.3 75.5 - - - +
162B ALA* 1.3 64.9 + - - +
169B ALA* 5.3 0.5 - - - +
170B GLU* 3.7 13.8 + - - +
171B ALA* 3.9 9.8 + - - +
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Residues in contact with ALA 162 (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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185A PRO* 3.9 35.4 - - + +
187A VAL* 4.5 14.8 - - + -
137B ASN 4.1 0.3 - - - +
138B HIS* 3.3 19.8 - - - +
139B ILE 4.9 0.2 + - - -
144B TYR* 3.9 1.9 + - - +
160B CYS* 3.6 3.8 - - - -
161B THR* 1.3 86.8 + - - +
163B ASP* 1.3 60.6 + - - +
164B ILE* 4.3 0.8 + - - -
169B ALA* 4.0 11.4 - - + -
170B GLU 3.6 7.4 - - - +
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Residues in contact with ASP 163 (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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106B ARG* 2.8 31.5 + - - -
136B ALA* 3.5 2.4 - - - -
137B ASN 2.7 29.6 + - - +
138B HIS* 2.8 22.5 + - - +
160B CYS* 4.1 2.6 - - - -
162B ALA* 1.3 74.4 - - - +
164B ILE* 1.3 61.2 + - - +
165B ALA* 3.1 20.4 + - - +
166B GLU 5.1 0.9 + - - -
168B GLU 3.7 3.3 - - - +
169B ALA* 3.6 2.3 - - - -
170B GLU* 3.0 28.0 + - - +
172B PHE* 4.0 19.6 - - + -
174B PHE* 4.0 7.0 - - + -
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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