Contacts of the strand formed by residues 156 - 161 (chain D) in PDB entry 1RD3
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 GLN 156 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.6 22.2 - - + +
19D GLY* 4.0 5.0 + - - -
20D SER* 3.2 22.0 + - - +
21D ASP* 2.6 29.8 + - - +
139D THR* 3.2 8.7 - - - +
140D GLY 3.1 38.4 + - - +
142D GLY 5.3 0.7 - - - +
144D LEU* 3.6 24.4 - - + +
152D PRO* 3.6 25.3 - - + +
154D VAL 2.8 17.6 + - - +
155D LEU* 1.3 76.5 + - - +
157D VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C THR* 5.3 5.8 - - - +
16D ILE* 4.4 1.1 - - - -
19D GLY* 3.2 5.1 - - - -
20D SER* 2.8 54.0 + - - +
21D ASP 4.1 0.7 - - - +
22D ALA* 3.9 21.8 - - + -
26D MET* 4.2 15.5 - - + -
137D ARG* 3.5 29.6 - - + +
138D VAL 3.5 4.0 - - - -
139D THR* 3.5 21.3 - - + -
156D GLN* 1.3 76.6 - - - +
158D VAL* 1.3 66.9 + - - +
159D ASN* 4.7 1.1 - - - +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 3.7 26.0 - - + -
18D GLU 4.2 8.5 - - - +
19D GLY* 4.1 1.1 - - - -
137D ARG* 3.5 1.2 - - - -
138D VAL* 2.8 51.2 + - + +
157D VAL* 1.3 78.3 - - - +
159D ASN* 1.3 69.0 + - - +
160D LEU* 3.8 24.5 + - + -
184D TYR* 5.5 0.2 - - - +
187D ARG 4.6 2.7 - - - +
188D GLY* 3.8 28.0 - - - -
189D ASP 4.4 6.7 - - - +
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Residues in contact with ASN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 3.2 82.9 + - - +
135D LYS* 4.7 3.1 - - + -
136D GLY 3.1 8.7 - - - +
137D ARG* 3.1 35.0 + - - +
157D VAL* 4.7 1.0 - - - +
158D VAL* 1.3 76.2 - - - +
160D LEU* 1.3 68.5 + - - +
184D TYR* 3.2 21.2 + - - -
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LYS* 4.1 2.9 - - - -
136D GLY* 2.8 36.6 + - - +
138D VAL* 4.2 10.8 - - + -
158D VAL* 3.8 16.3 + - + +
159D ASN* 1.3 83.6 - - - +
161D PRO* 1.3 68.4 - - + +
162D ILE 3.8 0.2 + - - -
183D ALA* 4.3 10.5 - - + +
184D GLY* 4.1 22.2 - - + +
188D GLY 3.3 30.7 - - - +
189D ASP* 4.1 20.4 - - - +
190D ALA 4.3 3.1 - - - +
199D PHE* 3.9 8.3 - - + -
228D TYR* 3.4 27.1 - - + +
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Residues in contact with PRO 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D GLY* 3.8 19.5 - - - +
134D TYR 3.3 7.0 - - - +
135D LYS* 3.8 13.2 - - + -
160D LEU* 1.3 86.7 - - + +
162D ILE* 1.3 66.0 + - - +
163D VAL* 5.7 0.2 - - + -
183D ALA* 3.2 2.3 - - - -
184D GLY* 2.9 83.0 + - + +
186D GLU* 4.9 7.0 - - - +
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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