Contacts of the strand formed by residues 179 - 183 (chain B) in PDB entry 4PRO
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 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B THR 3.7 0.3 - - - +
133B GLN* 3.3 2.5 - - - +
134B GLY* 2.8 40.6 + - - -
136B ALA 2.7 28.3 + - - -
138B MET* 3.6 13.9 - - - +
147B TRP* 3.8 20.3 - - - -
160B GLY 3.9 3.8 - - - -
169B ASN* 3.2 19.8 + - - -
177B ARG* 4.6 1.0 - - - +
178B SER* 1.3 72.5 + - - +
180B LEU* 1.3 62.8 + - - +
181B PHE* 4.3 0.3 + - - -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 4.5 16.2 - - + -
121B ALA* 4.0 16.8 - - + -
123B TYR* 3.9 17.3 - - - +
131B LEU* 4.1 17.0 - - + -
132B THR 3.2 4.5 - - - +
133B GLN* 3.6 25.8 - - + +
138B MET* 4.6 2.3 - - - +
147B TRP* 4.8 2.0 + - - -
158B ALA* 3.9 3.3 - - - +
159B SER* 3.0 21.4 + - - -
160B GLY 2.8 17.9 + - - +
178B SER* 3.8 18.6 - - - +
179B SER* 1.3 83.8 - - - +
181B PHE* 1.3 62.7 + - - +
118D SER* 5.5 2.2 - - - -
163D LEU* 4.0 24.5 - - + -
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Residues in contact with PHE 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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100B VAL* 5.3 0.2 - - + -
114B ILE* 4.5 15.9 - - + -
131B LEU* 3.5 8.5 - - - +
132B THR* 2.9 70.2 + - + -
134B GLY 5.1 1.8 - - - -
147B TRP* 3.4 52.0 - + + -
155B GLN* 3.6 38.8 - - + -
156B GLY* 3.8 7.2 - - - -
157B VAL 3.2 19.7 - - - +
159B SER* 4.1 1.1 - - - +
179B SER 4.9 0.7 - - - -
180B LEU* 1.3 76.0 - - - +
182B GLU* 1.3 72.8 + - - +
183B ARG* 3.8 4.8 + - + -
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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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62B ASN* 3.5 3.9 - - - +
63B ASP* 3.2 41.5 + - + +
64B ARG* 2.6 44.4 + - - +
129B ARG 4.5 5.0 - - - +
130B GLY 4.6 3.6 - - - +
131B LEU* 3.4 22.1 - - + +
156B GLY* 3.0 2.9 - - - -
157B VAL* 2.8 37.7 + - + +
159B SER* 4.6 2.2 - - - -
181B PHE* 1.3 72.7 - - - +
183B ARG* 1.3 75.0 + - - +
184B LEU* 4.4 0.2 - - - -
187B ILE* 3.9 12.8 - - + -
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Residues in contact with ARG 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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93B GLU* 3.1 38.3 + - - +
117B LYS* 5.7 2.5 - - - -
118B ASN 6.0 2.2 - - - +
130B GLY 4.1 18.1 + - - +
132B THR* 3.6 25.6 - - - +
155B GLN 3.7 7.0 - - - +
181B PHE* 3.8 4.4 + - + +
182B GLU* 1.3 81.2 + - - +
184B LEU* 1.3 62.9 + - - +
185B GLN* 4.5 7.2 - - - +
186B PRO* 3.4 44.0 - - + +
187B ILE* 3.4 15.6 - - - +
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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