Contacts of the strand formed by residues 149 - 153 (chain C) in PDB entry 6BW4
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 VAL 149 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C THR 3.4 16.4 - - - +
143C LYS* 3.9 13.9 - - + +
147C SER 4.3 1.3 - - - +
148C ASP* 1.3 75.2 - - - +
150C LEU* 1.3 66.9 + - - +
173C LEU* 2.8 48.0 + - + +
176C HIS* 4.2 6.5 - - + -
183C LEU* 4.0 22.2 - - + -
193C LEU* 4.1 16.6 - - + -
195C SER* 3.7 15.9 - - - +
205C TRP* 3.6 24.2 - - + -
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C HIS* 4.1 5.2 - - + +
124C GLU* 5.0 4.7 - - + +
140C ILE 3.8 0.2 - - - +
141C ALA* 3.2 5.7 - - - +
142C THR* 2.8 36.4 + - - +
144C THR* 3.6 25.8 - - + -
148C ASP* 3.8 12.6 - - + -
149C VAL* 1.3 82.1 - - - +
151C VAL* 1.3 65.8 + - - +
152C PHE* 3.5 33.7 - - + -
167C CYS* 4.0 16.6 - - - -
169C PRO* 4.0 7.9 - - + -
171C LEU 3.6 2.0 - - - -
172C ARG* 3.5 39.3 - - + +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 5.6 3.1 - - - +
139C ILE* 3.5 32.3 - - + -
140C ILE 3.4 5.8 - - - +
141C ALA* 4.6 9.6 - - + -
150C LEU* 1.3 80.2 - - - +
152C PHE* 1.3 61.1 + - - +
169C PRO 3.8 0.7 - - - -
170C ASP* 2.8 35.0 + - + +
171C LEU* 3.1 27.9 + - + +
173C LEU* 3.8 29.8 - - + -
185C TRP* 4.7 7.6 - - + -
193C LEU* 4.8 0.2 - - + -
207C ILE* 4.6 13.5 - - + -
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Residues in contact with PHE 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LEU* 4.1 24.9 - - + -
121C ILE* 3.8 27.1 - - + -
122C ASN 3.9 6.7 - - - -
123C HIS* 3.8 22.7 - + + -
138C CYS 3.4 2.1 - - - +
139C ILE* 3.4 3.3 - - - +
140C ILE* 2.7 42.3 + - + +
142C THR* 3.8 10.5 - - + -
150C LEU* 3.5 27.6 - - + -
151C VAL* 1.3 78.1 - - - +
153C ASP* 1.3 61.7 + - - +
154C TYR* 3.7 2.2 + - + +
157C HIS* 3.8 20.9 - + + +
167C CYS* 3.8 22.0 - - - -
168C ASN 4.4 3.1 - - - -
169C PRO* 3.8 20.9 - - + -
170C ASP* 3.4 2.9 - - - +
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Residues in contact with ASP 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 5.6 1.4 - - - +
74A ASP* 6.1 0.9 - - - +
126A GLU* 4.7 4.0 - - - +
145A PRO* 5.6 1.4 - - - +
136C ASN* 5.3 2.8 + - - -
138C CYS* 3.4 15.2 - - - +
139C ILE* 3.7 23.6 - - + +
151C VAL* 5.1 0.2 - - - +
152C PHE* 1.3 69.0 - - - +
154C TYR* 1.3 60.0 + - - +
155C THR* 2.8 21.6 + - - -
156C LYS* 3.0 52.9 + - + +
157C HIS* 3.2 12.6 + - - -
170C ASP* 2.9 16.8 + - + +
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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