Contacts of the strand formed by residues 116 - 122 (chain Q) in PDB entry 5OOM
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 ILE 116 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114Q GLY 4.1 3.8 - - - +
115Q SER* 1.3 75.4 - - - +
117Q LEU* 1.3 64.5 + - - +
134Q LEU* 3.7 25.4 - - + -
135Q GLY 3.1 13.7 - - - +
136Q ILE* 4.7 2.0 - - + -
176Q VAL* 3.8 1.6 - - - +
177Q VAL* 2.9 40.4 + - + -
178Q LYS* 3.2 32.5 + - + +
180Q GLU* 3.4 25.4 - - - +
200Q PHE* 3.8 39.0 - - + -
204Q MET* 4.0 9.9 - - + -
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Residues in contact with LEU 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111Q PHE* 3.7 36.6 - - + -
115Q SER* 3.3 32.1 - - - +
116Q ILE* 1.3 80.1 - - - +
118Q ARG* 1.3 60.8 + - - +
119Q VAL* 4.8 3.6 - - + -
133Q PHE 3.6 1.0 - - - +
134Q LEU* 2.9 28.1 - - - +
135Q GLY 2.9 11.4 + - - +
137Q CYS* 4.3 5.8 - - + +
149Q PHE* 3.9 18.4 - - + -
151Q LEU* 3.8 13.8 - - + +
174Q ILE* 3.8 24.5 - - + -
175Q GLN 3.6 10.5 - - - +
176Q VAL* 4.5 6.5 - - + -
177Q VAL* 4.5 1.3 - - - -
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Residues in contact with ARG 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117Q LEU* 1.3 74.5 - - - +
119Q VAL* 1.3 65.6 + - - +
120Q THR* 4.3 2.5 + - + +
132Q GLN* 3.3 41.8 + - + +
133Q PHE 3.1 12.3 - - - +
134Q LEU* 3.4 20.8 - - + +
173Q GLU* 3.9 1.7 - - - +
174Q ILE* 3.7 1.0 - - - -
175Q GLN* 2.9 70.1 + - + +
177Q VAL* 4.3 1.5 - - + +
202Q VAL 2.9 26.0 + - - -
203Q ASN* 3.7 5.6 - - - +
204Q MET 2.8 32.3 + - - +
206Q PRO* 5.4 2.2 - - - +
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Residues in contact with VAL 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Q LEU* 4.8 4.5 - - + -
118Q ARG* 1.3 80.6 - - - +
120Q THR* 1.3 66.5 + - - +
121Q THR* 3.8 13.1 + - + +
131Q SER 3.3 1.4 - - - +
132Q GLN* 3.1 3.9 - - - -
133Q PHE* 2.9 32.0 + - - +
149Q PHE* 4.2 21.3 - - + -
151Q LEU* 4.8 1.6 - - + -
164Q PHE* 3.8 36.6 - - + -
171Q VAL* 4.5 7.0 - - + -
173Q GLU 3.4 8.3 - - - +
174Q ILE* 4.1 28.9 - - + -
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Residues in contact with THR 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Q ARG* 5.4 2.9 - - + +
119Q VAL* 1.3 74.5 - - - +
121Q THR* 1.3 61.1 + - - +
130Q ILE* 4.4 15.7 - - + -
131Q SER 2.9 7.2 - - - -
132Q GLN* 3.6 33.9 - - + +
171Q VAL* 3.6 3.5 - - - -
172Q GLN* 2.8 31.2 + - - +
173Q GLU* 2.8 51.6 + - + +
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Residues in contact with THR 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L MET* 3.9 9.9 - - + -
119Q VAL* 3.8 4.8 + - + +
120Q THR* 1.3 77.8 - - - +
122Q ALA* 1.3 69.5 + - - +
130Q ILE* 3.1 3.6 - - - -
131Q SER* 2.9 44.6 + - - -
164Q PHE* 3.6 31.6 - - + -
170Q ARG* 3.3 5.6 - - - -
171Q VAL* 3.7 20.2 - - + -
172Q GLN* 3.3 5.8 - - - -
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Residues in contact with ALA 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E ILE 3.9 12.3 - - - +
346E THR* 4.7 9.2 - - + -
347E PHE* 4.5 13.0 - - + +
121Q THR* 1.3 86.2 + - - +
123Q ASP* 1.3 61.7 + - - +
124Q PRO* 4.1 1.9 - - - +
128Q GLY* 5.7 0.7 - - - -
129Q LYS 3.8 7.9 - - - +
130Q ILE* 4.1 5.8 - - + -
170Q ARG* 2.9 32.6 + - + +
172Q GLN* 3.1 22.0 + - - +
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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