Contacts of the strand formed by residues 117 - 122 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 5.5 0.9 - - - -
220A SER 5.8 3.4 - - - -
115B PRO 4.0 0.4 + - - -
116B PRO* 1.3 79.1 - - - +
118B MET* 1.3 63.9 + - - +
131B PHE* 3.4 4.5 - - - +
132B LEU* 2.7 46.7 + - - +
133B ALA 5.2 0.2 - - - -
134B PRO* 5.7 0.4 - - - +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 3.7 15.9 - - - +
219A PRO 4.7 4.8 + - - +
220A SER* 5.5 4.9 + - - -
116B PRO 4.9 0.7 - - - +
117B GLY* 1.3 75.8 - - - +
119B GLN* 1.3 64.8 + - - +
120B VAL* 3.7 16.8 - - + -
129B MET* 4.4 5.4 - - + +
130B ARG 3.3 13.9 - - - +
131B PHE* 3.9 23.3 - - + -
132B LEU* 5.6 0.4 - - - -
156B VAL* 6.0 0.4 - - - -
189B VAL* 3.7 33.0 - - + +
190B GLN 5.0 0.9 - - - -
191B VAL* 4.0 20.2 - - + -
205B SER* 4.3 13.2 - - - +
208B VAL* 3.6 36.2 - - + +
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Residues in contact with GLN 119 (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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122A VAL 3.7 18.0 + - - -
123A LEU* 3.7 13.1 - - + +
124A ALA* 3.5 21.1 + - - +
217A THR* 6.1 0.5 - - - +
218A VAL* 3.7 29.7 + - + +
219A PRO* 4.8 13.8 - - + +
118B MET* 1.3 74.4 - - - +
120B VAL* 1.3 64.9 + - - +
121B GLU* 3.5 25.5 + - - +
129B MET* 3.1 4.3 - - - +
130B ARG* 2.9 39.5 + - + +
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Residues in contact with VAL 120 (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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118B MET* 3.7 32.3 - - + -
119B GLN* 1.3 81.3 - - - +
121B GLU* 1.3 83.4 + - - +
127B LEU* 4.3 24.2 - - + -
128B HIS 3.3 9.2 - - - +
129B MET* 3.9 8.3 - - + -
189B VAL* 3.8 13.7 - - + -
208B VAL* 4.1 17.3 - - + +
210B GLU* 4.3 25.0 - - + +
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Residues in contact with GLU 121 (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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121A GLU* 3.7 21.4 - - + +
122A VAL 4.9 1.3 - - - +
123A LEU* 3.6 32.8 - - + -
119B GLN* 3.5 20.4 + - - +
120B VAL* 1.3 85.0 - - - +
122B VAL* 1.3 66.4 + - - +
123B LEU* 3.7 16.3 - - + +
127B LEU* 3.6 2.4 - - - -
128B HIS 2.7 36.4 + - - +
210B GLU* 6.3 0.2 - - - -
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Residues in contact with VAL 122 (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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119A GLN* 4.1 8.3 + - - -
121A GLU* 5.2 2.6 - - - +
121B GLU* 1.3 74.3 + - - +
123B LEU* 1.3 64.1 + - - +
124B ALA* 3.8 24.0 + - - +
126B CYS 3.7 6.3 - - - +
127B LEU* 3.4 20.2 - - + -
210B GLU* 3.5 32.3 - - + +
211B GLN 3.6 22.7 - - - +
212B THR* 3.8 4.5 - - - -
213B THR* 4.3 9.4 - - + +
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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