Contacts of the strand formed by residues 106 - 110 (chain L) in PDB entry 3KDM
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 106 (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* 3.1 19.7 + - - +
7L PRO* 2.6 24.3 + - - +
8L ALA 3.6 0.4 - - - -
9L SER 3.9 0.7 - - - -
10L VAL* 3.6 40.8 - - + +
20L ILE* 3.4 27.8 - - + +
86L ALA 3.7 0.2 - - - +
87L ASP* 3.3 5.0 + - - +
88L TYR* 2.7 39.9 + - - +
105L GLY* 1.3 73.8 - - - -
107L LYS* 1.3 65.4 + - - +
108L VAL 3.7 1.4 + - - -
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Residues in contact with LYS 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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8L ALA 3.0 14.8 + - - +
9L SER* 3.3 9.3 - - - -
10L VAL 2.9 22.9 + - - +
86L ALA 3.6 5.8 - - - +
87L ASP* 3.3 31.1 + - - +
106L THR* 1.3 70.6 - - - +
108L VAL* 1.3 72.4 + - - +
109L GLU* 3.7 6.3 + - + +
169L GLU* 3.0 40.0 + - - +
177L TYR* 6.0 1.6 - - - +
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Residues in contact with VAL 108 (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 VAL* 3.1 7.2 - - + +
18L ILE* 3.6 30.5 - - + -
20L ILE* 3.5 22.2 - - + -
77L ILE* 4.6 2.2 - - + -
80L LEU* 4.1 14.4 - - + -
84L ASP 4.2 8.7 - - - +
85L GLU* 3.6 22.3 - - - +
86L ALA 2.9 12.3 + - - +
88L TYR* 3.5 34.3 - - + -
107L LYS* 1.3 80.0 - - - +
109L GLU* 1.3 61.6 + - - +
110L ILE* 4.1 10.5 - - + -
170L GLN* 4.1 0.5 - - - +
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Residues in contact with GLU 109 (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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9L SER* 6.3 2.0 - - - -
10L VAL 2.9 8.2 + - - +
11L SER* 3.0 42.7 - - - -
12L GLY 3.2 5.5 + - - -
107L LYS* 3.7 7.6 + - + +
108L VAL* 1.3 73.9 - - - +
110L ILE* 1.3 69.4 + - - +
111L LYS* 4.6 1.2 - - - +
144L TYR* 2.8 28.8 + - - -
145L PRO* 6.0 0.2 - - - +
146L ARG* 4.4 7.1 + - - +
170L GLN* 3.2 18.8 - - - +
177L TYR* 2.3 34.1 + - - +
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Residues in contact with ILE 110 (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 GLY 3.5 3.1 - - - +
14L PRO* 4.0 24.5 - - + -
80L LEU* 3.3 30.1 - - + -
81L GLN 3.3 24.2 - - - +
82L ALA* 3.7 20.9 - - - +
85L GLU* 4.2 14.1 - - + +
108L VAL* 4.1 8.5 - - + -
109L GLU* 1.3 78.3 - - - +
111L LYS* 1.3 73.2 + - - +
112L ARG* 3.8 0.4 + - + -
144L TYR* 3.8 3.5 + - - -
170L GLN* 2.7 32.8 + - - +
175L SER* 4.1 19.5 - - - +
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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