Contacts of the strand formed by residues 137 - 142 (chain B) in PDB entry 4MCA
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 PHE 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B VAL* 3.7 25.4 - - + -
131B TYR* 3.6 14.5 - + + -
132B THR* 5.0 1.2 - - - +
136B GLU* 1.3 76.0 - - - +
138B ALA* 1.3 72.6 + - - +
139B GLU* 3.5 33.0 - - - -
140B TYR* 3.7 22.4 - + - -
258B ASN* 3.4 50.5 - - + +
261B THR* 2.8 20.7 + - - +
334B GLU* 3.9 11.4 - - + -
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Residues in contact with ALA 138 (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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130B ILE* 2.8 34.7 + - + +
131B TYR* 4.1 9.6 - - - -
132B THR* 4.1 12.6 - - + +
136B GLU 3.2 0.8 + - - -
137B PHE* 1.3 85.0 - - - +
139B GLU* 1.3 65.6 + - + +
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Residues in contact with GLU 139 (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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129B VAL* 3.8 1.7 - - - -
130B ILE* 2.8 45.3 + - + +
137B PHE* 3.5 14.2 - - - -
138B ALA* 1.3 84.2 - - + +
140B TYR* 1.3 65.0 + - - +
141B LEU* 3.9 26.3 - - - +
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Residues in contact with TYR 140 (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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127B LEU* 3.6 26.7 - - + -
128B SER 3.9 1.8 - - - -
129B VAL* 4.1 20.2 - - + -
137B PHE* 3.8 22.0 - + - -
139B GLU* 1.3 80.7 - - - +
141B LEU* 1.3 60.9 + - - +
142B ILE* 3.8 10.2 + - + +
190B MET* 3.6 20.0 - - + -
250B LEU* 3.8 18.7 - - + +
254B HIS* 3.8 17.0 - - - +
258B ASN* 3.3 24.7 + - - -
333B GLY 6.2 0.4 - - - -
334B GLU* 4.5 5.4 + - - -
335B THR* 4.3 18.1 + - + -
1001B GOL 4.3 11.0 - - - -
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Residues in contact with LEU 141 (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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106B TYR* 5.5 9.6 - - + +
127B LEU* 3.3 4.0 - - - -
128B SER* 2.8 44.3 + - - +
130B ILE* 4.1 24.7 - - + -
139B GLU* 3.8 17.6 + - - +
140B TYR* 1.3 71.0 - - - +
142B ILE* 1.3 69.0 + - - +
143B TYR* 3.8 34.6 + - + +
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Residues in contact with ILE 142 (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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6B GLN* 6.1 1.6 - - - +
126B ALA* 3.5 9.2 - - + +
127B LEU* 3.5 28.3 - - + -
140B TYR* 3.8 9.1 + - + +
141B LEU* 1.3 79.8 - - - +
143B TYR* 1.3 75.9 + - - +
144B PRO* 4.1 2.6 - - - +
190B MET* 4.1 39.0 - - + +
246B GLU* 6.1 0.2 - - - +
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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