Contacts of the strand formed by residues 103 - 107 (chain L) in PDB entry 3LS5
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 103 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6L GLN* 3.4 17.6 + - - +
7L SER 4.0 6.9 + - - -
8L PRO* 2.8 35.0 + - + +
9L THR 3.6 4.5 - - - +
11L MET* 4.7 3.6 - - + +
21L ILE* 3.9 38.0 - - + +
85L ALA 3.7 0.3 - - - +
86L THR* 3.3 3.6 - - - -
87L TYR* 2.8 35.2 + - - -
102L GLY* 1.3 72.9 - - - -
104L LYS* 1.3 72.2 + - - +
105L LEU* 3.7 4.1 + - + +
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Residues in contact with LYS 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L THR 3.1 13.5 + - - +
10L THR* 3.3 9.5 + - - +
11L MET 2.9 27.5 + - - +
85L ALA 3.8 5.8 - - - +
86L THR* 3.9 19.0 - - + +
102L GLY 4.1 0.8 - - - -
103L THR* 1.3 74.8 - - - +
105L LEU* 1.3 59.4 + - - +
106L GLU* 3.9 35.9 + - + +
143L LYS* 5.6 2.6 - - - +
166L ASP* 3.7 25.8 + - - +
167L GLN 6.1 0.2 - - - +
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Residues in contact with LEU 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L MET* 3.7 39.3 - - + +
13L ALA* 4.2 11.7 - - + -
19L ILE* 4.1 12.1 - - + -
21L ILE* 5.3 6.1 - - + -
76L ILE* 3.5 32.3 - - + -
79L MET* 3.5 26.0 - - + -
83L ASP 3.9 2.5 - - - +
84L VAL* 3.4 8.0 - - - +
85L ALA 2.9 33.3 + - - +
87L TYR* 3.8 20.0 - - + -
103L THR* 3.7 2.9 + - + +
104L LYS* 1.3 72.2 - - - +
106L GLU* 1.3 62.3 + - - +
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Residues in contact with GLU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L THR* 3.9 9.9 + - - -
11L MET 2.8 11.3 + - - +
12L ALA* 3.4 7.4 - - + -
13L ALA* 2.9 29.5 + - - +
79L MET* 4.2 2.6 - - - +
84L VAL* 4.0 10.1 - - + -
104L LYS* 3.9 31.0 + - + +
105L LEU* 1.3 79.3 - - - +
107L LEU* 1.3 61.4 + - - +
143L LYS* 3.1 26.6 + - - -
167L GLN* 3.3 18.8 + - + +
174L TYR* 2.7 38.7 + - - +
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Residues in contact with LEU 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ALA* 5.3 1.3 - - - -
13L ALA 3.5 7.0 - - - +
15L PRO* 4.1 21.3 - - + -
79L MET* 3.7 32.8 - - + -
81L ALA* 4.0 33.2 - - + +
84L VAL* 3.6 13.4 - - + +
106L GLU* 1.3 74.5 - - - +
108L LYS* 1.3 73.8 + - - +
141L TYR* 3.7 9.0 + - - -
167L GLN* 2.7 35.2 + - - +
172L SER* 3.4 21.9 - - - +
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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