Contacts of the strand formed by residues 154 - 163 (chain A) in PDB entry 3WYR
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A SER* 4.2 16.5 + - - +
125A SER 3.4 16.4 - - - +
126A GLN* 3.5 19.7 - - + +
148A VAL 3.7 0.5 - - - +
149A PRO* 3.6 2.8 - - - +
150A SER* 2.7 53.6 + - - +
151A ILE 3.9 1.0 + - - -
152A ASN* 3.2 24.3 + - + +
153A GLY* 1.3 74.5 - - - +
155A PHE* 1.3 64.9 + - - +
156A GLN* 4.9 3.8 + - - -
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Residues in contact with PHE 155 (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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124A SER* 3.3 2.1 - - - -
125A SER 2.9 20.7 + - - -
126A GLN 4.4 4.9 - - - -
127A SER 3.3 26.0 - - - +
128A SER* 3.3 33.2 - - - -
129A PHE 3.9 15.3 - - - +
132A TYR* 2.9 24.9 + - - +
147A ALA* 4.2 14.1 - - + -
148A VAL 3.4 4.5 - - - -
149A PRO* 4.4 29.2 - - + -
153A GLY 4.8 6.5 - - - -
154A THR* 1.3 78.4 - - - +
156A GLN* 1.3 61.0 + - - +
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Residues in contact with GLN 156 (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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108A ARG* 5.1 2.4 - - - +
122A SER* 3.6 27.4 + - - -
123A CYS 3.1 15.9 - - - +
124A SER* 3.9 16.8 + - - +
132A TYR* 4.0 4.4 - - - -
147A ALA* 3.6 0.2 - - - -
148A VAL* 2.9 42.5 + - + +
150A SER* 3.9 17.5 + - - +
154A THR* 4.9 4.3 + - - +
155A PHE* 1.3 75.4 - - - +
157A ALA* 1.3 63.2 + - - +
158A ASP* 3.6 16.0 + - - +
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Residues in contact with ALA 157 (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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121A LEU 3.5 2.3 - - - +
122A SER* 3.3 2.5 - - - -
123A CYS 2.9 32.3 + - - -
132A TYR* 3.5 31.0 - - + -
145A LEU* 4.1 13.7 - - + -
146A PRO 3.8 17.0 - - - +
148A VAL* 5.9 0.4 - - - -
156A GLN* 1.3 76.0 - - - +
158A ASP* 1.3 64.9 + - - +
159A PHE* 3.9 8.0 + - + -
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Residues in contact with ASP 158 (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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108A ARG* 3.1 21.6 + - - +
120A THR* 4.0 11.5 - - + +
121A LEU 3.6 4.0 - - - -
122A SER* 2.6 24.3 + - - -
145A LEU* 3.3 17.4 - - - +
156A GLN* 3.6 16.9 + - - +
157A ALA* 1.3 77.1 + - - +
159A PHE* 1.3 61.9 + - - +
160A PRO* 3.2 15.0 - - + +
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Residues in contact with PHE 159 (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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119A VAL 3.9 0.3 - - - +
120A THR* 3.4 4.0 - - - -
121A LEU 2.9 43.3 + - - +
123A CYS* 4.4 9.6 - - - -
132A TYR* 3.5 39.0 - - + -
134A LEU* 3.7 39.9 - - + -
143A LEU* 3.7 41.3 - - + -
145A LEU* 3.5 33.7 - - + -
157A ALA* 3.9 15.7 - - + -
158A ASP* 1.3 70.6 - - - +
160A PRO* 1.3 64.9 - - + +
161A LEU* 3.5 10.3 + - + +
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Residues in contact with PRO 160 (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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119A VAL 4.1 0.4 - - - +
120A THR* 3.7 20.0 - - + +
143A LEU* 5.8 1.9 - - - +
145A LEU* 5.3 6.1 - - + -
158A ASP* 3.2 14.6 - - + +
159A PHE* 1.3 80.9 - - - +
161A LEU* 1.3 64.2 + - - +
162A GLY 3.3 4.2 + - - +
201A NAG 5.8 2.5 - - - +
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Residues in contact with LEU 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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119A VAL* 3.2 26.4 + - + +
121A LEU* 3.7 18.2 - - + -
134A LEU* 4.0 21.1 - - + -
143A LEU* 4.1 21.1 - - + -
159A PHE* 3.9 8.7 - - + +
160A PRO* 1.3 76.5 - - - +
162A GLY* 1.3 64.7 + - - +
163A PRO* 3.9 6.8 - - - +
170A TYR* 3.4 39.0 - - + +
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Residues in contact with GLY 162 (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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118A ASN* 3.1 30.2 - - - +
119A VAL* 3.4 7.8 + - - +
160A PRO* 3.3 5.9 + - - +
161A LEU* 1.3 80.7 - - - +
163A PRO* 1.3 76.7 - - - +
164A ALA* 3.5 1.2 + - - +
201A NAG 3.9 15.9 + - - -
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Residues in contact with PRO 163 (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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116A GLY* 3.7 21.1 - - - +
117A GLU 3.4 6.3 - - - +
118A ASN* 3.3 9.1 - - - +
161A LEU* 4.2 5.7 - - - +
162A GLY* 1.3 84.1 - - - +
164A ALA* 1.3 62.5 + - - +
165A THR* 3.5 11.3 + - - +
201A NAG 4.3 14.4 - - - -
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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