Contacts of the strand formed by residues 117 - 123 (chain A) in PDB entry 3LQM
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 GLY 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PRO 3.9 0.4 + - - -
116A PRO* 1.3 78.5 - - - +
118A MET* 1.3 65.1 + - - +
131A PHE* 3.5 5.0 - - - +
132A LEU* 2.8 48.0 + - - +
134A PRO* 5.8 0.2 - - - +
191A VAL* 4.3 0.7 - - - +
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Residues in contact with MET 118 (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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116A PRO 5.0 0.4 - - - +
117A GLY* 1.3 77.2 - - - +
119A GLN* 1.3 63.2 + - - +
120A VAL* 3.9 17.8 + - + +
129A MET* 4.3 6.3 - - + +
130A ARG 3.4 11.7 - - - +
131A PHE* 3.7 24.9 - - + -
132A LEU* 4.3 6.3 - - - +
156A VAL* 6.0 0.4 - - - -
189A VAL* 3.3 45.3 - - + +
190A GLN 4.5 1.3 - - - +
191A VAL* 4.0 17.0 - - + -
205A SER* 4.4 12.8 - - - +
208A VAL* 3.9 24.4 - - + +
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Residues in contact with GLN 119 (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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118A MET* 1.3 72.5 - - - +
120A VAL* 1.3 63.6 + - - +
121A GLU* 4.4 15.9 + - - +
128A HIS 3.8 0.5 - - - +
129A MET* 3.2 4.7 - - - +
130A ARG* 2.9 76.6 + - + +
132A LEU* 5.5 1.3 - - + +
122B VAL 4.1 14.5 + - - -
123B LEU* 3.3 28.2 - - + +
124B ALA 4.6 2.2 - - - +
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Residues in contact with VAL 120 (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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118A MET* 3.9 35.6 + - + +
119A GLN* 1.3 79.0 - - - +
121A GLU* 1.3 80.9 + - - +
127A LEU* 4.5 19.1 - - + -
128A HIS 3.3 12.1 - - - +
129A MET* 4.3 8.3 - - + -
189A VAL* 4.2 10.8 - - + -
208A VAL* 4.2 12.3 - - + -
210A GLU* 4.2 31.2 - - + +
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Residues in contact with GLU 121 (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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119A GLN* 4.4 15.2 + - + +
120A VAL* 1.3 83.0 - - - +
122A VAL* 1.3 68.9 + - - +
123A LEU* 4.0 15.9 - - + -
127A LEU* 3.6 2.4 - - - -
128A HIS* 2.7 43.1 + - + +
121B GLU* 3.7 21.0 - - + +
122B VAL 5.2 2.7 - - - +
123B LEU* 3.7 32.8 - - + -
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Residues in contact with VAL 122 (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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121A GLU* 1.3 79.6 + - - +
123A LEU* 1.3 66.1 + - - +
124A ALA 3.6 20.7 + - - +
126A CYS 3.3 9.4 - - - +
127A LEU* 3.7 17.0 - - + -
210A GLU* 4.1 21.1 - - + +
211A GLN 3.6 18.4 - - - +
212A THR* 3.7 5.2 - - - -
213A THR* 3.6 24.4 + - + +
119B GLN* 3.7 12.1 + - - -
121B GLU* 4.9 1.7 - - - +
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Residues in contact with LEU 123 (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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121A GLU* 4.0 13.2 - - + +
122A VAL* 1.3 81.0 - - - +
124A ALA* 1.3 71.7 + - - +
126A CYS* 2.8 28.6 + - - +
128A HIS* 3.9 31.2 - - + +
119B GLN* 3.7 19.1 - - - +
121B GLU* 3.6 27.4 - - + -
128B HIS* 3.8 24.2 - - + +
129B MET 4.0 1.8 - - - -
130B ARG* 3.4 36.8 - - + +
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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