Contacts of the strand formed by residues 16 - 21 (chain I) in PDB entry 2LMN
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15H GLN 3.3 5.9 + - - -
16H LYS* 3.3 38.9 - - + +
17H LEU* 2.9 27.4 + - - +
14I HIS* 3.9 17.2 + - + -
15I GLN* 1.3 88.8 - - - +
17I LEU* 1.3 60.1 + - - +
18I VAL* 5.4 5.6 - - + -
14J HIS* 6.3 1.3 - - - -
16J LYS* 3.6 26.7 - - + +
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Residues in contact with LEU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 3.3 34.5 - - + +
16I LYS* 1.3 74.6 - - - +
18I VAL* 1.3 76.6 + - - +
19I PHE* 4.5 13.5 - - + +
16J LYS 2.9 16.1 + - - +
17J LEU* 3.4 26.1 - - + -
18J VAL* 2.9 26.4 + - - +
36K VAL* 5.7 12.6 - - + -
36L VAL* 5.4 11.7 - - + -
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Residues in contact with VAL 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU 2.9 12.5 + - - +
18H VAL* 3.6 22.5 - - + -
19H PHE* 2.9 29.9 + - - +
16I LYS* 5.4 4.5 - - + -
17I LEU* 1.3 83.8 - - - +
19I PHE* 1.3 67.6 + - - +
20I PHE* 4.9 7.9 - - + +
16J LYS* 6.5 0.9 - - + -
18J VAL* 3.6 27.1 - - + -
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Residues in contact with PHE 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE* 3.2 37.5 - + + -
17I LEU* 4.7 11.9 - - + -
18I VAL* 1.3 75.8 - - - +
20I PHE* 1.3 64.7 + - - +
21I ALA* 4.8 9.4 - - + -
18J VAL* 2.8 17.6 + - - +
19J PHE* 3.9 18.4 - + + -
20J PHE* 2.9 32.4 + - - +
32K ILE* 5.2 6.3 - - + -
34K LEU* 3.1 40.4 - - + -
36K VAL* 5.4 3.1 - - + -
32L ILE* 4.5 13.0 - - + -
34L LEU* 3.2 39.5 - - + -
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Residues in contact with PHE 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE* 2.9 17.7 + - - +
20H PHE* 3.2 41.3 - + + -
21H ALA* 3.0 24.5 + - - +
22H GLU* 5.7 0.7 - - - -
18I VAL* 4.2 9.4 - - + -
19I PHE* 1.3 77.0 - - - +
21I ALA* 1.3 61.0 + - - +
22I GLU* 3.0 50.3 - - + -
20J PHE* 3.3 28.9 - + + -
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Residues in contact with ALA 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ALA* 3.8 9.0 - - + -
19I PHE* 4.8 8.3 - - + -
20I PHE* 1.3 74.9 - - - +
22I GLU* 1.3 73.4 + - - +
20J PHE 3.0 10.1 + - - +
21J ALA* 3.7 1.5 - - + -
22J GLU 3.0 19.4 + - - +
32K ILE* 3.8 29.2 - - + -
32L ILE* 4.3 16.6 - - + -
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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