Contacts of the strand formed by residues 16 - 21 (chain N) in PDB entry 2LMQ
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 16 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15M GLN 3.8 3.8 + - - -
16M LYS* 3.6 39.0 - - + +
17M LEU* 2.8 28.3 + - - +
13N HIS* 4.3 8.7 + - - -
14N HIS* 3.1 32.8 + - + +
15N GLN* 1.3 86.2 - - - +
17N LEU* 1.3 65.8 + - - +
18N VAL* 5.6 3.6 - - + -
16O LYS* 4.1 34.4 - - + +
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Residues in contact with LEU 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M LEU* 3.3 22.4 - - + -
19M PHE* 6.1 2.0 - - + -
15N GLN* 3.4 40.4 - - + +
16N LYS* 1.3 82.9 - - - +
18N VAL* 1.3 66.1 + - - +
19N PHE 4.3 0.2 - - - -
15O GLN* 5.4 4.3 - - + -
16O LYS* 2.8 32.1 + - - +
17O LEU* 3.3 32.2 - - + -
18O VAL* 3.0 17.2 + - - +
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Residues in contact with VAL 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M LEU 2.8 15.1 + - - +
18M VAL* 3.4 24.2 - - + -
19M PHE* 2.8 36.7 + - - +
20M PHE* 5.4 4.5 - - + -
16N LYS* 5.6 3.4 - - + -
17N LEU* 1.3 81.2 - - - +
19N PHE* 1.3 66.0 + - - +
20N PHE* 4.9 7.9 - - + +
16O LYS* 5.6 4.9 - - - -
18O VAL* 3.8 27.6 - - + +
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Residues in contact with PHE 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.4 32.5 - + + -
21M ALA* 4.1 28.3 - - + -
32M ILE* 4.0 26.7 - - + -
18N VAL* 1.3 76.4 - - - +
20N PHE* 1.3 66.5 + - - +
21N ALA* 4.3 11.2 - - + -
17O LEU* 6.3 0.9 - - + -
18O VAL* 2.7 29.3 + - - +
19O PHE* 3.4 17.3 - + + -
20O PHE* 2.9 18.3 + - - +
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Residues in contact with PHE 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE 2.9 9.4 + - - +
20M PHE* 3.4 37.8 - + + -
21M ALA* 2.7 34.1 + - - +
22M GLU* 5.7 0.2 - - - +
18N VAL* 4.3 5.4 - - + -
19N PHE* 1.3 77.9 - - - +
21N ALA* 1.3 65.0 + - - +
22N GLU* 3.9 20.8 - - + +
20O PHE* 2.9 59.2 - + + -
22O GLU* 3.9 16.6 - - - -
22P GLU* 5.4 0.2 - - - -
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Residues in contact with ALA 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M ALA* 3.5 11.0 - - + +
29M GLY 3.5 21.8 - - - +
30M ALA* 4.6 7.6 - - + -
32M ILE* 6.5 0.2 - - + -
19N PHE* 4.3 16.2 - - + -
20N PHE* 1.3 78.2 - - - +
22N GLU* 1.3 61.5 + - - +
24N VAL* 6.1 0.2 - - + -
20O PHE 2.7 14.8 + - - +
21O ALA* 3.3 7.5 - - + -
22O GLU* 2.9 25.5 + - - +
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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