Contacts of the strand formed by residues 143 - 147 (chain B) in PDB entry 3LMK
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 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 3.7 30.1 - - + +
38B GLY* 4.0 6.5 - - - +
94B GLU* 4.1 16.6 - - + +
112B PHE* 3.5 53.4 + - + +
115B ASP 5.1 0.4 + - - -
141B LYS 4.9 3.6 - - - +
142B PRO* 1.3 75.7 - - - +
144B VAL* 1.3 63.7 + - - +
145B GLY 3.7 19.1 - - - +
146B VAL* 3.8 19.7 - - + -
167B ILE* 3.7 24.3 - - + +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.8 22.4 - - + -
36B ILE 3.1 15.2 + - - +
37B ILE* 5.4 2.0 - - + -
142B PRO* 4.4 14.6 - - + +
143B ILE* 1.3 76.8 - - - +
145B GLY* 1.3 58.6 + - - +
166B ASN 5.0 0.5 - - - +
167B ILE* 3.9 5.0 - - - +
168B PRO* 3.6 20.3 - - - +
407B MET* 5.3 1.6 - - - -
411B LEU* 3.8 21.8 - - + -
432B ILE* 3.8 26.0 - - + +
434B GLY* 5.5 1.7 - - - -
437B LEU* 3.4 25.8 - - + +
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Residues in contact with GLY 145 (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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36B ILE 4.5 0.6 + - - -
37B ILE* 3.5 6.7 - - - +
38B GLY* 2.7 32.2 + - - -
143B ILE* 3.6 1.7 - - - +
144B VAL* 1.3 79.2 - - - +
146B VAL* 1.3 58.3 + - - +
167B ILE* 3.6 3.8 - - - -
168B PRO* 3.2 15.7 - - - -
407B MET* 3.7 20.2 - - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY* 3.2 7.4 - - - +
40B LEU* 4.1 23.8 - - + -
112B PHE* 3.9 22.4 - - + -
143B ILE* 3.8 19.1 - - + -
145B GLY* 1.3 78.8 - - - +
147B ILE* 1.3 78.7 + - - +
148B GLY 4.3 5.8 - - - +
158B VAL* 4.9 0.2 - - + -
162B LEU* 3.8 31.0 - - + -
167B ILE* 4.2 2.9 - - + -
168B PRO 3.1 6.8 + - - +
169B GLN* 3.3 3.8 - - + +
170B ILE 2.9 25.8 + - - -
407B MET* 3.7 2.5 - - - +
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Residues in contact with ILE 147 (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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37B ILE* 4.0 11.7 - - + -
38B GLY 2.8 17.1 + - - +
39B ALA* 3.3 7.8 - - + +
40B LEU 3.0 27.7 + - - +
41B PHE* 4.4 10.7 - - + -
72B MET* 4.3 3.8 - - + -
146B VAL* 1.3 73.1 - - - +
148B GLY* 1.3 60.8 + - - +
170B ILE* 3.4 11.9 - - + +
172B TYR* 3.8 23.8 - - + -
400B VAL* 4.9 1.3 - - + +
403B ALA* 3.6 35.0 - - + +
404B ILE* 4.0 24.0 - - + -
407B MET* 4.0 25.1 - - + -
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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