Contacts of the strand formed by residues 141 - 147 (chain C) in PDB entry 4QKB
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 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C PRO* 1.3 77.4 - - - +
142C VAL* 1.3 62.9 + - - +
158C LEU* 3.8 3.1 - - - +
159C LEU* 2.7 46.8 + - - +
179C ILE* 4.0 16.8 - - - +
185C SER* 4.9 0.2 - - - -
192C ILE* 3.8 7.5 - - - +
194C ARG* 3.8 20.4 - - - +
197C ARG* 3.3 32.8 + - - -
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Residues in contact with VAL 142 (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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141C SER* 1.3 77.9 - - - +
143C MSE 1.3 62.8 + - - +
144C ARG 3.8 1.0 + - - -
156C GLU* 4.2 22.7 - - + -
157C LEU 3.7 9.0 - - - +
158C LEU* 4.7 1.6 - - + -
179C ILE* 3.5 7.3 - - - +
180C LEU* 3.1 42.5 + - + +
185C SER* 4.0 9.5 + - - +
186C PHE 3.5 36.3 - - - +
187C PHE* 3.9 10.5 - - + +
192C ILE* 3.8 24.9 - - + -
194C ARG* 5.3 0.4 - - - +
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Residues in contact with MSE 143 (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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141C SER 4.2 0.6 + - - -
142C VAL* 1.3 73.0 - - - +
144C ARG* 1.3 65.6 + - - +
145C LEU* 4.1 3.2 + - + -
156C GLU* 3.4 1.9 - - - -
157C LEU* 2.8 54.4 + - + +
159C LEU* 3.8 11.4 - - + +
165C TYR* 3.6 50.3 - - + +
167C LEU* 4.0 17.7 - - - -
177C HIS* 4.2 15.3 - - + -
178C GLU 3.2 13.9 - - - +
179C ILE* 3.4 30.7 - - + +
302C AKG 3.7 15.0 - - + +
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Residues in contact with ARG 144 (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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120C PRO* 5.9 0.4 - - - +
142C VAL 3.8 3.0 + - - -
143C MSE 1.3 71.9 - - - +
145C LEU* 1.3 66.6 + - - +
146C VAL* 4.2 13.4 - - + +
154C TRP* 4.7 11.2 - - + -
155C LEU 3.2 17.3 - - - +
156C GLU* 4.0 24.8 + - + +
176C SER 3.7 0.9 - - - +
177C HIS* 3.5 1.9 - - - -
178C GLU* 3.1 67.8 + - + +
180C LEU* 3.8 31.6 - - + +
184C GLU* 4.9 10.9 + - - +
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Residues in contact with LEU 145 (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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29C LEU* 5.6 0.2 - - + -
33C ALA* 4.0 19.5 - - + -
143C MSE 4.8 4.5 - - + -
144C ARG* 1.3 75.2 - - - +
146C VAL* 1.3 61.8 + - - +
154C TRP* 3.2 8.7 - - - +
155C LEU* 2.9 49.4 + - + +
157C LEU* 3.8 27.4 - - + -
167C LEU* 3.9 14.6 - - + -
171C ALA* 3.8 24.2 - - + +
175C PHE* 4.1 17.9 - - + -
176C SER 3.1 8.7 - - - +
177C HIS* 3.7 25.1 - - + -
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Residues in contact with VAL 146 (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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120C PRO* 5.8 1.8 - - + -
144C ARG* 4.2 14.8 - - + +
145C LEU* 1.3 78.4 - - - +
147C HIS* 1.3 75.1 + - - +
148C THR 3.5 0.2 + - - -
151C PRO* 3.8 29.4 - - + +
153C GLU 3.8 4.7 - - - +
154C TRP* 4.5 6.5 - - + +
175C PHE* 3.1 6.0 - - - -
176C SER* 2.7 48.1 + - - +
178C GLU* 4.2 19.1 - - - +
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Residues in contact with HIS 147 (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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28C ARG* 3.3 32.7 + - - -
146C VAL* 1.3 79.3 - - - +
148C THR* 1.3 66.8 + - - +
149C GLN* 3.3 37.2 + - + +
150C GLU* 3.2 38.9 - - + +
151C PRO* 4.0 1.6 - - - +
153C GLU* 3.0 25.1 + - + +
174C ASP* 3.6 19.1 + - + +
175C PHE* 3.4 30.7 - + + -
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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