Contacts of the strand formed by residues 163 - 169 (chain A) in PDB entry 1LHO
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 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A HIS* 3.4 7.7 - - - +
18A LEU* 2.8 29.5 + - - -
19A SER* 4.7 0.8 + - - -
47A ARG 3.2 12.8 - - - -
48A THR* 3.8 6.3 - - - -
161A LEU* 2.9 13.9 + - - -
162A ASP* 1.3 77.2 + - - +
164A CYS* 1.3 65.7 + - - -
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Residues in contact with CYS 164 (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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15A ALA* 4.6 1.1 - - + -
16A VAL 3.2 3.1 - - - -
17A HIS* 4.4 6.3 - - - -
18A LEU* 4.6 1.5 - - - +
46A VAL* 3.2 10.8 - - - +
47A ARG* 2.8 45.6 + - + +
100A TRP* 3.5 20.4 - - + -
163A GLY* 1.3 78.0 - - - -
165A LEU* 1.3 60.1 + - - +
188A CYS* 2.0 49.8 - - + -
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Residues in contact with LEU 165 (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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14A PRO 4.3 0.2 - - - +
15A ALA* 3.2 3.3 - - - -
16A VAL* 2.8 55.2 + - + +
18A LEU* 4.0 27.6 - - + +
44A PHE* 3.4 45.3 - - + -
45A GLU 3.5 3.8 - - - +
46A VAL* 5.0 1.1 - - + -
55A ILE* 5.2 2.9 - - + -
100A TRP* 4.5 0.2 - - - -
143A LEU* 3.9 22.4 - - + -
164A CYS* 1.3 74.7 - - - +
166A ARG* 1.3 63.8 + - - +
168A ASP* 3.8 28.7 - - + +
170A TRP* 4.3 6.1 - - + -
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Residues in contact with ARG 166 (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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13A PRO* 4.3 37.5 + - - +
14A PRO 3.4 19.5 - - - +
15A ALA* 3.7 6.3 - - + -
44A PHE* 3.7 2.1 - - - +
45A GLU* 2.5 56.0 + - + +
100A TRP* 3.5 59.9 - - + +
165A LEU* 1.3 77.1 - - - +
167A ARG* 1.3 75.4 + - + +
168A ASP* 3.1 8.2 + - - -
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Residues in contact with ARG 167 (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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13A PRO* 4.4 22.2 - - + +
14A PRO 4.4 3.6 + - - -
43A SER* 3.6 4.2 + - - +
44A PHE* 3.4 11.3 + - - -
45A GLU* 3.0 38.7 + - + -
102A GLN* 5.3 8.7 - - - +
166A ARG* 1.3 86.4 - - + +
168A ASP* 1.3 62.4 + - - +
169A SER* 4.0 1.0 + - - -
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Residues in contact with ASP 168 (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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16A VAL* 6.3 0.2 - - - -
43A SER 3.1 4.9 - - - -
44A PHE* 3.7 16.6 - - + -
143A LEU* 4.4 4.0 - - - +
165A LEU* 3.8 19.9 - - + +
166A ARG* 4.2 2.4 - - - -
167A ARG* 1.3 80.3 + - - +
169A SER* 1.3 60.8 + - - +
170A TRP* 2.7 35.4 + - + +
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Residues in contact with SER 169 (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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39A LYS* 3.4 22.8 + - - -
42A SER* 3.2 7.0 - - - -
43A SER* 2.9 40.4 + - - +
167A ARG 5.2 0.7 - - - -
168A ASP* 1.3 76.0 - - - +
170A TRP* 1.3 64.8 + - - +
171A LEU 4.1 1.0 + - - -
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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