Contacts of the helix formed by residues 98 - 108 (chain A) in PDB entry 2LCK
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 GLY 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL 3.0 3.0 + - - -
96A ARG 3.1 0.6 - - - -
97A ILE* 1.3 87.3 - - - +
99A LEU* 1.3 52.4 + - - +
100A TYR 3.1 0.7 - - - -
101A ASP* 2.4 22.5 - - - +
102A SER* 2.4 32.7 + - - -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 2.8 38.2 + - + +
96A ARG* 5.2 1.1 - - + -
98A GLY* 1.3 70.2 - - - -
100A TYR* 1.3 61.5 + - - +
102A SER* 4.0 7.6 - - - -
103A VAL* 3.4 33.9 + - + +
130A ALA* 3.7 32.8 - - + +
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL 4.1 1.8 + - - -
96A ARG* 3.4 59.4 - - + +
98A GLY 3.1 0.8 - - - -
99A LEU* 1.3 77.8 - - - +
101A ASP* 1.3 58.6 + - + +
102A SER 3.2 1.1 - - - -
104A LYS* 2.7 73.0 + - + +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG 4.5 0.7 - - - +
97A ILE 3.6 8.6 - - - +
98A GLY* 2.4 42.4 + - - +
100A TYR* 1.3 81.7 - - + +
102A SER* 1.3 66.1 + - - +
104A LYS* 4.4 3.1 - - - -
105A GLN* 2.7 58.4 + - - +
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLY* 2.4 28.4 + - - -
99A LEU* 4.1 7.0 - - - -
101A ASP* 1.3 81.5 + - - +
103A VAL* 1.3 67.2 + - - +
104A LYS 3.2 0.9 - - - -
105A GLN* 4.2 3.0 - - - +
106A PHE* 3.3 29.3 + - - +
126A THR* 5.7 0.2 - - - -
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.4 36.8 + - + +
100A TYR 4.9 0.2 - - - +
102A SER* 1.3 74.8 - - - +
104A LYS* 1.3 65.2 + - - +
106A PHE* 3.3 8.7 + - + +
107A TYR* 3.3 23.5 + - + +
123A GLY* 5.4 5.2 - - - +
126A THR* 4.0 30.5 - - + +
127A GLY* 5.3 4.7 - - - +
130A ALA* 5.3 6.1 - - + -
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 2.7 64.3 + - + +
101A ASP* 4.1 3.6 - - - +
102A SER 3.2 0.2 - - - -
103A VAL* 1.3 78.5 - - - +
105A GLN* 1.3 57.2 + - + +
106A PHE 3.1 4.3 - - - -
107A TYR* 3.4 3.3 + - - +
108A THR* 3.2 37.8 + - - +
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Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP* 2.7 49.6 + - - +
102A SER* 4.3 2.9 - - - +
104A LYS* 1.3 72.9 - - + +
106A PHE* 1.3 61.6 + - - +
107A TYR 3.3 0.4 - - - -
108A THR* 4.3 2.5 - - - +
109A LYS* 3.4 33.4 + - - +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 3.3 21.6 + - - +
103A VAL* 3.4 10.8 - - - +
104A LYS 3.1 0.2 - - - -
105A GLN* 1.3 81.1 - - - +
107A TYR* 1.3 56.6 + - + +
109A LYS* 4.6 19.8 - - - +
119A ARG* 4.5 5.4 - - - +
122A ALA* 3.6 37.2 - - + +
123A GLY* 5.8 1.8 - - - +
126A THR* 3.9 30.5 - - + -
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 3.3 14.9 + - + +
104A LYS* 3.4 3.3 + - - +
105A GLN 3.3 0.2 - - - -
106A PHE* 1.3 78.0 - - - +
108A THR* 1.3 69.9 + - - +
109A LYS 3.4 2.0 - - - -
116A ILE* 5.3 0.2 - - - +
119A ARG* 2.8 75.2 + - + -
120A LEU* 5.4 2.7 - - + -
123A GLY* 5.3 5.4 - - - -
190A ASN* 5.1 13.0 - - - -
193A GLU* 6.1 3.8 - - + -
194A LEU* 3.3 36.9 - - + +
197A TYR* 3.9 47.3 - + + -
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Residues in contact with THR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 3.2 25.1 + - - +
105A GLN* 4.5 1.6 - - - -
107A TYR* 1.3 84.9 - - - +
109A LYS* 1.3 65.8 + - - +
110A GLY* 3.2 4.5 + - - -
119A ARG* 5.6 2.2 - - - +
197A TYR* 4.9 13.9 + - - +
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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