Contacts of the strand formed by residues 171 - 179 (chain B) in PDB entry 3BPL
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 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B SER* 4.0 3.3 + - - -
141B GLU* 3.0 52.3 + - - +
170B ILE* 1.3 75.6 - - - +
172B TYR* 1.3 64.0 + - - +
195B LYS* 5.3 4.3 - - - -
196B TRP 3.3 18.6 - - - -
197B HIS* 4.1 12.5 - - - -
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Residues in contact with TYR 172 (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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138B ILE* 4.1 13.2 - - + -
139B TRP* 3.3 24.7 - - - +
140B SER* 3.6 19.7 - - - -
146B ASP* 5.3 4.0 - - - -
165B THR 4.3 2.4 + - - -
166B LEU* 3.4 27.9 - - + -
167B LYS* 2.8 52.2 + - - +
170B ILE* 3.9 8.8 - - + +
171B SER* 1.3 75.2 - - - +
173B ARG* 1.3 62.4 + - - +
195B LYS* 3.0 4.0 - - - +
196B TRP* 2.8 71.5 + + + -
198B ASN* 4.3 11.0 - - - -
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Residues in contact with ARG 173 (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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138B ILE* 3.3 5.2 - - - +
139B TRP* 2.8 68.6 + - + +
141B GLU* 3.2 43.7 + - + +
172B TYR* 1.3 76.0 - - - +
174B ALA* 1.3 62.2 + - - +
193B SER* 3.1 25.7 + - - +
194B THR 3.3 6.3 - - - +
195B LYS* 3.4 33.6 - - + +
196B TRP* 4.0 1.6 - - - -
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Residues in contact with ALA 174 (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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104B LEU* 3.4 17.2 - - + +
116B LEU* 4.4 12.3 - - + -
136B VAL* 4.7 1.3 - - + -
137B ASN 3.1 10.3 - - - +
138B ILE* 4.1 10.1 - - + -
139B TRP* 4.5 0.7 - - - -
173B ARG* 1.3 76.7 - - - +
175B ARG* 1.3 62.6 + - - +
193B SER* 3.0 7.7 - - - -
194B THR* 2.7 37.1 + - - +
196B TRP* 3.8 18.2 - - + -
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Residues in contact with ARG 175 (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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104B LEU* 3.4 10.1 - - - +
136B VAL* 3.6 1.5 - - - +
137B ASN* 2.8 59.9 + - + +
139B TRP* 3.7 20.0 - - + -
174B ALA* 1.3 79.1 - - - +
176B VAL* 1.3 62.6 + - - +
190B TRP* 3.3 57.1 - - + +
191B SER* 3.6 20.4 - - - +
192B PRO 4.4 0.4 - - - -
193B SER* 4.1 6.1 - - - -
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Residues in contact with VAL 176 (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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101B PRO* 3.5 23.3 - - + +
102B GLY* 5.9 0.2 - - - -
104B LEU* 4.5 8.7 - - + -
118B TRP* 3.9 26.2 - - + -
134B TYR* 3.9 13.2 - - + -
135B ALA 3.1 21.1 - - - +
136B VAL* 3.7 17.3 - - + -
175B ARG* 1.3 76.2 - - - +
177B ARG* 1.3 72.9 + - - +
190B TRP* 3.5 4.3 - - - -
191B SER* 2.9 42.3 + - - +
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Residues in contact with ARG 177 (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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101B PRO* 3.7 4.9 - - - -
134B TYR* 3.4 8.5 - - - +
135B ALA* 3.2 31.8 + - + +
149B ILE* 5.6 9.1 - - - +
151B GLN* 6.1 0.6 - - - +
176B VAL* 1.3 77.6 - - - +
178B ALA* 1.3 63.1 + - - +
187B TRP* 3.4 59.8 - - + +
188B SER* 3.4 20.1 + - - +
189B GLU 3.7 6.3 - - - +
190B TRP* 3.4 51.6 - - + +
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Residues in contact with ALA 178 (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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98B PRO* 4.0 5.6 - - + +
99B ARG 4.9 3.1 - - - +
101B PRO* 3.7 10.1 - - + +
132B LEU* 4.3 15.5 - - + -
133B THR 3.6 6.7 - - - +
134B TYR* 3.4 29.8 - - + -
177B ARG* 1.3 77.0 - - - +
179B TRP* 1.3 61.2 + - - +
187B TRP* 3.5 5.2 - - - -
188B SER* 2.9 35.9 + - - +
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Residues in contact with TRP 179 (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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98B PRO* 4.1 3.6 - - - -
132B LEU* 3.4 6.2 - - - -
133B THR* 3.1 57.8 + - - +
178B ALA* 1.3 76.6 - - - +
180B ALA* 1.3 59.6 + - - +
181B GLN* 3.5 55.6 - - + +
184B ASN* 4.7 10.5 - - - -
185B THR* 3.3 34.8 - - - -
186B THR 3.7 13.5 - - - +
187B TRP* 3.5 41.4 - + + -
183C ARG* 5.2 0.8 - - - +
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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