Contacts of the strand formed by residues 150 - 157 (chain A) in PDB entry 3CMM
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 ARG 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLN* 3.1 23.9 + - - +
125A VAL* 3.4 6.8 - - + -
126A VAL* 2.9 25.8 + - - +
148A GLY* 3.7 19.3 + - - -
149A ILE* 1.3 75.0 - - - +
151A PHE* 1.3 59.0 + - - +
166A ASP 3.8 4.5 - - - -
167A LEU* 3.4 42.8 + - + +
168A GLY* 5.5 0.4 - - - -
170A GLU 3.0 26.5 + - - -
171A PHE* 3.6 26.5 - - + +
377A ALA* 3.9 26.0 + - + +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A VAL* 3.4 11.2 - - + -
128A ALA* 4.0 18.6 - - + -
137A LYS* 3.8 20.2 - - + -
140A ILE* 3.9 19.1 - - + -
141A ASN* 3.5 50.3 - - + +
144A CYS* 4.0 16.4 - - + -
145A HIS 5.6 0.2 - - - +
149A ILE 3.6 0.9 + - - +
150A ARG* 1.3 75.6 - - - +
152A ILE* 1.3 69.8 + - - +
153A SER* 3.8 30.7 - - - -
164A PHE* 4.0 20.0 - + - -
166A ASP* 2.7 43.6 + - - +
269A LEU* 4.4 3.8 - - + -
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.0 11.7 - - + -
126A VAL 2.9 8.8 + - - +
127A VAL* 3.0 13.2 - - + -
128A ALA* 2.8 23.9 + - - +
151A PHE* 1.3 84.4 - - - +
153A SER* 1.3 64.2 + - - +
163A THR* 4.1 10.5 - - - +
164A PHE 3.3 10.1 - - - +
165A VAL* 4.3 18.4 - - + -
167A LEU* 4.6 4.3 - - + -
370A VAL* 3.8 25.4 - - + -
373A GLU* 3.7 13.7 - - + +
374A VAL* 3.6 42.0 - - + +
377A ALA* 4.5 5.8 - - + -
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 5.0 0.9 - - - -
128A ALA* 3.1 13.9 - - - -
137A LYS* 4.0 19.5 + - - +
151A PHE* 3.8 22.8 - - - -
152A ILE* 1.3 77.8 - - - +
154A SER* 1.3 61.6 + - - +
162A ASN* 5.2 2.6 + - - -
163A THR* 3.2 7.4 + - - -
164A PHE* 2.7 49.4 + - - +
269A LEU* 5.1 2.9 - - - +
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.4 23.2 - - - +
51A ILE* 5.1 2.5 - - - -
127A VAL* 5.8 0.7 - - - -
128A ALA 3.1 6.0 + - - -
129A THR* 3.4 7.8 - - - +
130A ASP 3.3 19.1 + - - -
137A LYS* 4.2 3.2 + - - +
153A SER* 1.3 77.6 + - - +
155A GLU* 1.3 60.4 + - - +
162A ASN* 2.9 21.4 + - - -
163A THR* 4.1 0.7 - - - +
366A PHE* 3.5 17.8 - - - +
370A VAL* 3.6 24.0 - - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.0 5.2 - - - -
130A ASP* 4.0 15.3 - - + -
134A LEU* 5.8 0.2 - - - +
137A LYS* 3.2 21.5 + - - +
154A SER* 1.3 76.3 + - - +
156A THR* 1.3 62.3 + - - +
157A ARG* 2.6 34.4 + - + +
161A GLY* 3.3 2.9 - - - -
162A ASN* 3.0 39.5 + - - +
296A PHE* 3.6 30.1 - - + -
299A LEU* 4.6 2.3 - - - +
300A HIS* 2.8 33.9 + - - -
366A PHE* 5.1 0.9 - - - -
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.4 12.9 - - + +
130A ASP* 4.2 13.8 - - - +
155A GLU* 1.3 77.2 + - - +
157A ARG* 1.3 84.6 + - - +
158A GLY 5.2 1.6 - - - +
160A PHE 3.6 4.2 + - - -
161A GLY* 4.3 0.2 - - - -
357A GLY 4.6 7.0 - - - +
358A ASP* 4.1 13.5 - - - +
359A ILE 5.3 0.9 - - - +
362A VAL* 3.3 30.0 + - + +
363A VAL* 3.8 28.0 - - + +
366A PHE* 4.4 6.1 - - - +
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP* 3.5 42.0 + - - +
155A GLU* 2.6 38.4 + - - +
156A THR* 1.3 86.8 + - - +
158A GLY* 1.3 66.1 + - - +
160A PHE* 3.0 33.7 + - - +
296A PHE* 3.8 22.0 - - + -
299A LEU* 4.5 14.8 - - + +
300A HIS* 4.5 6.9 + - - -
310A LEU* 3.6 30.8 - - - +
351A LEU* 4.4 10.3 - - + -
354A GLN* 3.5 4.7 - - - +
355A ALA* 3.6 23.3 + - - +
357A GLY 3.8 4.9 - - - -
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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