Contacts of the strand formed by residues 160 - 168 (chain A) in PDB entry 3ORH
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 LEU 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY* 3.4 9.4 - - - -
129A PHE 3.4 14.1 - - - +
131A GLY* 4.2 3.4 - - - -
132A ILE* 3.8 25.4 - - + -
156A ALA 3.2 21.1 + - - +
158A ARG 3.4 0.6 - - - -
159A LEU* 1.3 77.3 - - - +
161A LYS* 1.3 65.2 + - - +
162A PRO* 4.7 0.3 - - - +
164A GLY 3.8 15.3 - - - +
165A VAL 3.8 25.1 - - - +
166A LEU* 4.0 17.0 - - + +
202A PHE* 4.0 26.7 - - + -
233A VAL 4.4 0.2 - - - +
235A LYS* 2.9 35.0 + - + -
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Residues in contact with LYS 161 (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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62A GLY* 5.9 0.2 - - - -
63A ARG* 3.7 25.5 - - - +
127A GLY* 3.3 23.8 - - - +
128A HIS 3.8 5.8 - - - -
129A PHE 2.9 17.8 + - - +
130A ASP* 3.3 40.8 + - - +
159A LEU 3.8 0.4 + - - -
160A LEU* 1.3 76.6 - - - +
162A PRO* 1.4 79.2 - - + +
163A GLY 3.2 0.2 + - - -
164A GLY* 2.8 17.4 + - - +
235A LYS* 3.7 6.1 - - - +
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Residues in contact with PRO 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY* 5.5 2.7 - - - +
160A LEU 4.7 0.7 - - - +
161A LYS* 1.4 90.5 - - + +
163A GLY* 1.3 59.0 + - - +
164A GLY 3.4 0.3 + - - -
235A LYS* 4.4 10.9 - - + +
236A GLY 3.7 19.7 - - - +
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Residues in contact with GLY 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 3.6 29.6 + - - +
161A LYS 3.2 0.2 + - - -
162A PRO* 1.3 71.4 - - - +
164A GLY* 1.3 63.2 + - - +
165A VAL* 3.9 0.9 + - - +
234A THR* 3.7 14.9 - - - +
235A LYS 2.9 21.9 + - - -
236A GLY 4.0 1.4 + - - -
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Residues in contact with GLY 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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60A LYS* 5.0 1.1 - - - -
129A PHE 4.5 1.8 - - - -
130A ASP* 3.3 17.7 - - - -
160A LEU* 3.8 15.4 - - - +
161A LYS* 2.8 18.8 + - - +
162A PRO 3.2 1.4 + - - -
163A GLY* 1.3 79.2 - - - +
165A VAL* 1.3 59.6 + - - -
233A VAL 3.8 0.5 - - - +
234A THR* 3.3 2.9 - - - -
235A LYS* 2.9 25.2 + - - +
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Residues in contact with VAL 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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56A ALA* 3.3 30.1 - - + +
57A ALA* 4.3 8.2 - - - +
59A SER* 3.5 12.3 - - - +
60A LYS* 3.7 17.3 - - + -
130A ASP 2.9 15.0 + - - +
131A GLY* 3.2 4.3 - - - -
132A ILE 2.9 24.6 + - - +
160A LEU* 3.8 4.4 - - - +
163A GLY 5.0 0.7 - - - +
164A GLY* 1.3 72.6 - - - -
166A LEU* 1.3 72.9 + - - +
208A ARG* 5.5 0.4 - - - +
232A LEU* 4.3 20.2 - - + -
233A VAL 3.6 11.4 - - - +
234A THR* 4.5 9.0 - - - +
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Residues in contact with LEU 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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132A ILE* 3.6 28.3 - - + +
134A TYR* 4.8 3.8 - - + -
151A PHE* 4.6 5.4 - - + -
152A ILE* 3.8 42.2 - - + -
156A ALA* 4.0 15.3 - - + -
160A LEU* 4.0 15.0 - - + +
165A VAL* 1.3 73.8 - - - +
167A THR* 1.3 79.2 + - - +
168A TYR* 4.4 6.7 - - + -
197A LEU* 4.6 1.8 - - + -
202A PHE* 4.4 2.7 - - + -
231A PRO 3.7 0.3 - - - +
232A LEU* 3.7 3.3 - - - -
233A VAL* 2.7 60.5 + - + +
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Residues in contact with THR 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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53A LEU* 3.3 44.3 - - + +
56A ALA* 4.0 9.2 - - - -
57A ALA* 3.8 13.5 - - + +
132A ILE 2.9 19.4 + - - +
133A LEU* 3.9 11.2 - - + -
134A TYR 3.0 20.6 + - - -
165A VAL* 4.2 0.4 + - - -
166A LEU* 1.3 75.6 - - - +
168A TYR* 1.3 67.3 + - - +
230A THR* 3.7 4.7 - - - +
231A PRO* 2.7 25.2 + - - +
232A LEU* 5.3 0.2 - - - -
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Residues in contact with TYR 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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53A LEU* 3.8 7.2 - - - +
133A LEU* 5.5 0.4 - - - -
134A TYR* 3.1 30.3 - - + +
148A GLN* 3.7 26.9 - - + -
149A PHE* 4.4 1.3 - + - -
152A ILE* 3.7 24.2 - - + -
166A LEU* 4.4 9.4 - - + -
167A THR* 1.3 81.3 + - - +
169A CYS* 1.3 70.3 + - - +
174A TRP* 3.6 16.4 - + - -
189A PHE* 3.6 8.1 - + - -
193A GLN* 2.8 44.4 + - - +
197A LEU* 3.9 18.4 - - + +
231A PRO* 3.2 44.8 - - + +
233A VAL* 4.7 3.1 - - + -
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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