Contacts of the strand formed by residues 177 - 183 (chain B) in PDB entry 3DBL
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 LEU 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B ILE* 3.4 16.8 - - + +
143B CYS* 3.5 28.9 - - - -
154B ILE* 4.7 6.3 - - + -
155B ASN* 4.5 16.4 - - - +
158B LEU* 3.7 29.4 - - + -
175B VAL 4.5 0.7 - - - +
176B PRO* 1.3 74.0 - - - +
178B ILE* 1.3 64.4 + - - +
179B ASP* 3.8 5.4 + - + -
190B ARG 3.9 0.2 - - - +
191B VAL* 3.8 0.3 - - - -
192B ILE* 2.8 54.1 + - + +
194B PRO* 5.0 2.0 - - + -
200B ILE* 3.8 28.9 - - + -
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Residues in contact with ILE 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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140B ILE* 3.6 29.6 - - + -
141B ILE 3.0 4.7 + - - +
142B VAL* 3.2 7.4 - - + +
143B CYS* 2.8 24.6 + - - +
176B PRO* 4.2 0.7 - - + -
177B LEU* 1.3 83.2 - - - +
179B ASP* 1.3 62.3 + - - +
189B ALA* 5.9 0.2 - - + -
190B ARG 3.3 14.6 - - - +
191B VAL* 4.4 12.1 - - + -
303B CYS* 3.6 40.6 - - + +
306B GLU* 4.6 6.5 - - + -
307B VAL* 4.2 16.2 - - + -
310B ILE* 3.7 26.2 - - + -
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Residues in contact with ASP 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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143B CYS* 3.0 31.7 - - + +
145B LEU 4.4 0.9 + - - -
151B ARG* 3.2 40.8 + - - +
177B LEU* 3.8 10.4 + - + +
178B ILE* 1.3 74.6 - - - +
180B GLY* 1.3 68.4 + - - +
188B ASN* 4.0 5.5 + - - +
189B ALA* 3.6 1.0 - - - -
190B ARG* 3.0 44.8 + - + +
192B ILE* 5.7 2.0 - - + +
200B ILE* 5.6 8.3 - - + +
303B CYS* 4.0 4.7 - - - -
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Residues in contact with GLY 180 (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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59B LEU* 3.3 16.5 - - - +
143B CYS 3.2 12.9 + - - +
144B GLY* 4.4 0.9 - - - -
151B ARG* 3.1 14.9 + - - -
179B ASP* 1.3 84.3 - - - +
181B GLY* 1.3 59.3 + - - -
188B ASN* 3.1 10.5 - - - -
299B ILE* 3.9 5.4 - - - -
303B CYS* 3.7 17.1 - - - -
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Residues in contact with GLY 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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59B LEU* 3.9 2.2 - - - +
151B ARG* 3.5 8.7 - - - -
180B GLY* 1.3 74.8 - - - -
182B THR* 1.3 65.7 + - - -
187B GLY* 3.2 1.4 - - - -
188B ASN* 2.9 35.2 + - - +
299B ILE* 3.9 4.6 - - - +
173I LEU* 3.7 15.0 - - - -
175I GLY 3.4 10.3 - - - -
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Residues in contact with THR 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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59B LEU* 4.7 7.0 - - - -
181B GLY* 1.3 77.1 + - - -
183B GLU* 1.3 63.0 + - - +
184B GLY 5.6 0.7 - - - +
186B LYS 3.2 4.4 + - - -
187B GLY* 3.9 2.7 - - - -
289B ILE* 4.3 2.3 - - - +
291B ALA* 5.6 7.2 - - + +
295B THR* 2.8 38.6 + - + +
296B ASN* 3.0 33.2 - - - +
299B ILE* 4.2 1.6 - - - +
173I LEU* 3.9 4.5 - - - +
175I GLY* 2.9 29.5 + - - -
176I GLY* 3.1 15.0 - - - +
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Residues in contact with GLU 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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182B THR* 1.3 79.8 - - - +
184B GLY* 1.3 70.0 + - - +
185B PHE 3.0 0.9 + - - -
186B LYS* 2.8 31.6 + - - +
208B PRO* 5.3 2.2 - - - +
289B ILE* 3.9 20.5 - - + +
172I GLN 4.6 0.4 - - - +
173I LEU* 3.5 21.3 - - + +
174I ARG* 2.6 65.9 + - - +
175I GLY 3.5 9.6 - - - +
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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