Contacts of the strand formed by residues 109 - 117 (chain A) in PDB entry 1LKF
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 GLN 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.9 12.6 - - - +
108A PHE* 1.3 78.9 - - + +
110A VAL* 1.3 62.0 + - - +
111A GLN* 3.7 20.7 + - + +
143A ASN* 3.0 34.2 + - - +
144A TYR* 3.4 19.4 - - - -
145A LYS* 3.6 31.6 + - - +
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Residues in contact with VAL 110 (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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101A PRO* 4.4 10.5 - - + -
105A ASN* 3.6 35.2 - - + +
107A GLU 4.1 0.4 - - - +
109A GLN* 1.3 71.0 - - - +
111A GLN* 1.3 63.0 + - - +
112A ASN* 4.8 3.6 - - - +
142A ILE* 3.6 21.6 - - + +
143A ASN* 3.2 6.8 + - - -
144A TYR* 2.9 65.7 + - + +
146A GLN* 3.5 26.7 - - + +
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Residues in contact with GLN 111 (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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105A ASN* 5.3 1.0 - - - +
109A GLN* 3.7 20.9 + - + +
110A VAL* 1.3 76.5 - - - +
112A ASN* 1.3 71.7 + - - +
126A ASN* 3.5 6.5 + - - +
127A GLY* 2.8 32.6 + - - -
128A LEU* 3.6 35.8 + - + +
142A ILE 3.3 4.9 - - - -
143A ASN* 3.1 31.2 - - - +
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Residues in contact with ASN 112 (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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100A ALA* 4.0 12.1 - - + +
101A PRO* 3.5 29.8 - - - +
102A LYS* 4.4 1.9 + - - +
105A ASN* 5.1 4.9 - - - +
110A VAL* 4.8 3.9 - - - +
111A GLN* 1.3 93.2 + - - +
113A THR* 1.3 59.0 + - - +
124A ILE* 4.2 10.4 - - + +
125A SER 3.2 14.9 + - - +
126A ASN* 3.8 12.1 + - - +
127A GLY 3.1 9.0 + - - +
128A LEU* 4.3 0.7 - - - +
141A THR* 3.3 7.2 - - - -
142A ILE* 3.1 46.7 + - + +
226A LEU* 6.1 0.4 - - - -
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Residues in contact with THR 113 (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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112A ASN* 1.3 73.7 + - - +
114A LEU* 1.3 64.8 + - - +
115A GLY* 4.1 1.6 - - - +
123A SER 3.7 0.7 - - - +
124A ILE* 3.3 5.8 - - - +
125A SER* 2.9 46.4 + - - +
127A GLY 2.8 18.8 + - - -
128A LEU* 3.2 21.8 + - - +
139A SER* 3.8 19.5 - - - +
140A GLU 3.4 11.9 - - - +
141A THR* 3.8 6.5 - - + +
226A LEU* 5.5 0.4 - - - -
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Residues in contact with LEU 114 (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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52A VAL* 4.2 30.5 - - + -
99A TYR 4.5 6.5 - - - -
100A ALA* 4.6 1.8 - - + -
113A THR* 1.3 76.2 - - - +
115A GLY* 1.3 64.8 + - - +
116A TYR* 5.0 0.7 - - + +
122A ILE* 4.0 17.7 - - + -
123A SER 3.4 2.9 - - - -
124A ILE* 3.8 29.4 - - + -
138A PHE* 4.1 4.7 - - + +
139A SER* 3.4 4.0 + - - -
140A GLU 2.8 34.0 + - - +
226A LEU* 3.8 33.3 - - + +
228A VAL* 3.6 23.8 - - + -
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A THR* 4.1 3.1 - - - +
114A LEU* 1.3 77.5 - - - +
116A TYR* 1.3 61.1 + - - -
117A THR* 5.2 1.5 + - - -
121A ASP 3.5 1.4 - - - +
122A ILE* 3.4 5.9 - - - +
123A SER* 2.7 44.0 + - - -
136A THR* 5.1 9.4 - - - -
138A PHE 3.5 6.1 - - - -
139A SER* 4.5 5.4 - - - -
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Residues in contact with TYR 116 (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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16A VAL* 4.6 0.7 - - + -
41A ILE* 3.8 35.5 + - + +
43A ASP* 2.8 37.1 + - - +
46A TYR* 4.1 4.5 - - - +
48A LYS 5.2 1.2 + - - -
50A THR* 3.7 23.2 + - + -
114A LEU* 4.4 1.9 - - + +
115A GLY* 1.3 73.5 - - - -
117A THR* 1.3 74.4 + - - +
118A PHE* 4.3 2.2 - - - -
120A GLY* 3.4 30.2 - - - -
121A ASP 3.4 3.6 - - - -
122A ILE* 3.5 23.8 - - + -
136A THR* 3.5 5.3 - - - -
137A ALA* 2.9 37.6 + - + -
138A PHE* 2.9 26.7 + - + +
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Residues in contact with THR 117 (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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115A GLY 5.2 1.0 + - - -
116A TYR* 1.3 82.6 - - - +
118A PHE* 1.3 84.5 + - + +
120A GLY 2.9 17.8 + - - -
121A ASP* 2.9 33.4 + - + +
123A SER* 5.3 3.3 + - - -
136A THR* 4.4 17.2 - - - +
137A ALA 4.4 2.7 - - - +
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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