Contacts of the strand formed by residues 115 - 121 (chain B) in PDB entry 3QK3
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 LYS 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B HIS* 1.3 75.0 - - - +
116B LEU* 1.3 62.8 + - - +
117B HIS* 4.1 5.2 - - + +
130B GLU* 3.8 24.7 + - - +
131B ILE 3.3 7.9 - - - +
132B VAL* 4.2 20.0 - - + -
153B ALA 3.8 0.7 - - - -
154B ILE* 2.9 55.9 + - + +
155B ASN* 2.9 31.3 + - - +
158B TRP* 3.6 2.4 + - - -
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Residues in contact with LEU 116 (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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115B LYS* 1.3 73.4 - - - +
117B HIS* 1.3 66.0 + - - +
118B LEU* 3.7 23.3 - - + -
129B MET 3.6 1.2 - - - +
130B GLU* 3.5 0.5 - - - -
131B ILE* 2.8 47.3 + - + +
151B VAL* 3.5 25.1 - - + -
152B ARG 3.5 7.9 - - - +
153B ALA* 3.7 17.7 - - + -
158B TRP* 3.5 39.5 - - + -
173B PHE* 4.6 4.5 - - + -
194B VAL* 3.7 31.0 - - + -
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Residues in contact with HIS 117 (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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115B LYS* 4.1 9.1 - - + +
116B LEU* 1.3 81.7 - - - +
118B LEU* 1.3 62.8 + - - +
119B PHE* 3.7 23.5 - - + -
128B LYS* 3.5 29.0 + - - -
129B MET 3.3 3.8 - - - +
130B GLU* 2.8 43.0 + - + +
151B VAL* 3.4 8.3 - - - +
152B ARG* 2.8 45.1 + - + +
154B ILE* 4.1 25.0 - - + +
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Residues in contact with LEU 118 (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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116B LEU* 3.7 26.0 - - + -
117B HIS* 1.3 73.1 - - - +
119B PHE* 1.3 63.2 + - - +
128B LYS* 3.3 6.1 - - - +
129B MET* 2.9 41.2 + - + +
131B ILE* 4.0 20.6 - - + -
139B LEU* 3.5 40.8 - - + -
144B PHE* 3.4 13.8 - - + -
148B VAL* 4.1 11.2 - - + -
150B SER 4.0 2.2 - - - -
151B VAL* 3.9 22.2 - - + -
173B PHE* 5.8 1.1 - - + -
191B LEU* 5.6 4.0 - - + -
194B VAL* 4.4 7.0 - - + -
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Residues in contact with PHE 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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117B HIS* 3.7 29.2 - - + -
118B LEU* 1.3 76.6 - - - +
120B GLU* 1.3 60.8 + - - +
121B ASN 3.8 4.3 - - - +
124B PHE* 3.5 50.0 - + + -
125B SER 3.9 3.1 - - - +
126B GLY 4.3 4.5 - - - -
127B ARG 3.3 6.1 - - - -
128B LYS* 3.6 41.7 - - + -
144B PHE* 3.8 4.3 - - - -
148B VAL* 3.6 4.7 - - - +
149B ALA 2.9 25.6 + - - -
150B SER* 2.9 33.3 + - - +
151B VAL 4.5 0.2 - - - -
152B ARG* 3.6 24.9 - - + -
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Residues in contact with GLU 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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119B PHE* 1.3 72.8 - - - +
121B ASN* 1.3 73.6 + - - +
125B SER 3.7 0.8 + - - +
126B GLY* 3.7 5.6 - - - -
127B ARG* 3.0 47.2 + - + +
144B PHE* 3.7 10.6 - - + -
145B GLN* 5.1 6.9 - - - +
147B ARG* 2.9 42.4 + - + +
149B ALA* 3.4 6.3 - - - +
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Residues in contact with ASN 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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119B PHE* 3.8 0.7 - - - +
120B GLU* 1.3 100.0 + - - +
122B PRO* 1.4 66.5 - - + +
125B SER* 2.9 29.9 + - - +
126B GLY* 4.1 9.9 - - - +
147B ARG* 3.2 23.0 + - - -
149B ALA* 3.5 5.2 - - - -
150B SER* 2.6 27.0 + - - -
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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