Contacts of the strand formed by residues 113 - 117 (chain M) in PDB entry 1LK3
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 THR 113 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143I THR* 5.0 8.5 - - - +
111M ALA 4.6 2.8 + - - -
112M PRO* 1.3 73.1 - - - +
114M VAL* 1.3 64.8 + - - +
115M SER* 4.1 9.0 + - - +
134M LEU* 3.5 4.7 - - - +
136M ASN* 3.0 44.0 + - + +
137M ASN* 5.9 0.5 - - - +
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Residues in contact with VAL 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M PRO* 3.6 22.9 + - + +
113M THR* 1.3 76.9 - - - +
115M SER* 1.3 69.1 + - - +
133M CYS* 3.9 12.8 - - - -
134M LEU 3.2 8.3 - - - +
135M MET* 4.3 2.7 - - + -
193M CYS* 4.5 1.3 - - - +
195M VAL* 3.8 29.6 - - + -
204M VAL* 3.6 26.9 - - + -
206M LYS* 3.5 47.0 + - + +
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Residues in contact with SER 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I THR* 3.7 21.2 + - - +
113M THR* 4.7 7.6 + - - +
114M VAL* 1.3 78.5 + - - +
116M ILE* 1.3 62.5 + - - +
117M PHE* 3.7 27.1 - - - -
132M VAL 3.9 0.7 - - - +
133M CYS* 3.3 5.2 - - - -
134M LEU* 2.8 42.1 + - - +
136M ASN* 5.8 0.9 + - - -
206M LYS* 4.7 2.0 - - - -
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Residues in contact with ILE 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I PRO* 4.6 6.8 - - - +
133I GLY 4.7 1.9 + - - -
115M SER* 1.3 74.0 - - - +
117M PHE* 1.3 73.9 + - - +
118M PRO* 4.2 3.5 - - - +
131M VAL* 4.4 0.4 - - + -
132M VAL 3.4 8.5 - - - +
133M CYS* 4.4 0.7 - - - +
147M TRP* 3.7 21.1 - - + -
191M TYR 3.7 15.5 - - - +
192M THR 4.1 0.2 - - - -
193M CYS* 3.7 21.8 - - + +
206M LYS* 3.5 43.8 - - + +
207M SER 3.9 15.0 - - - +
208M PHE* 3.8 21.8 - - + -
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Residues in contact with PHE 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I LEU* 3.6 45.9 - - + +
131I ALA 3.6 26.0 - - - +
132I PRO* 3.9 4.7 - - + -
143I THR* 3.3 36.1 - - + -
144I LEU* 4.5 2.7 - - - -
115M SER* 3.7 26.2 - - - -
116M ILE* 1.3 80.1 - - - +
118M PRO* 1.3 70.2 - - + +
130M SER 4.5 0.2 - - - +
131M VAL* 3.4 6.1 - - - +
132M VAL* 2.7 49.0 + - + +
134M LEU* 3.7 26.0 - - + -
208M PHE* 4.1 3.4 - - - -
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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