Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 2YD7
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 GLU 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP 5.0 4.4 - - - +
155A PRO* 1.3 75.8 - - - +
157A ILE* 1.3 64.0 + - - +
158A THR* 4.0 8.5 + - + +
179A ARG* 3.8 6.1 + - - +
202A VAL 3.4 3.1 - - - +
203A ALA* 3.4 1.6 - - - -
204A THR* 2.8 44.6 + - + +
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Residues in contact with ILE 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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147A CYS* 3.6 11.0 - - + +
149A ALA* 3.9 22.7 - - + -
155A PRO 4.8 1.1 - - - +
156A GLU* 1.3 77.4 - - - +
158A THR* 1.3 65.7 + - - +
159A TRP* 3.8 21.3 - - + +
177A GLN* 2.6 32.8 + - - +
179A ARG* 3.6 29.5 - - - +
182A SER 3.8 8.3 - - - +
184A GLY* 3.6 32.8 - - - +
201A CYS* 3.8 21.8 - - - -
202A VAL 3.2 4.9 - - - +
203A ALA* 4.8 2.0 - - + -
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLU* 5.1 9.4 - - + +
157A ILE* 1.3 80.6 - - - +
159A TRP* 1.3 68.9 + - - +
160A PHE* 4.4 8.4 - - - -
166A VAL 6.1 0.4 - - - -
177A GLN* 3.9 8.5 - - - +
201A CYS* 3.6 2.4 - - - -
202A VAL* 2.7 52.2 + - - +
204A THR* 5.1 3.9 + - - +
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Residues in contact with TRP 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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132A PRO* 3.9 11.0 - - + -
145A MET* 3.7 37.0 - - + -
146A LEU 3.9 4.9 - - - -
147A CYS* 3.7 21.5 - - + -
157A ILE* 3.8 13.6 - - + +
158A THR* 1.3 82.5 - - - +
160A PHE* 1.3 69.5 + - - +
165A PRO* 3.6 1.7 - - - +
166A VAL* 2.9 38.2 + - + +
177A GLN* 3.8 23.0 + - - +
184A GLY 3.7 20.2 - - - -
185A ALA 4.1 1.6 - - - -
186A LEU* 3.7 46.0 - - + +
199A TYR* 4.3 14.1 - - + -
200A GLU 3.4 17.7 - - - -
201A CYS* 3.9 14.4 - - + -
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Residues in contact with PHE 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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42A SER* 3.9 26.7 - - - -
44A ILE* 4.4 13.0 - - + -
81A VAL* 4.8 2.2 - - + -
83A ARG* 5.4 0.7 - - - -
158A THR* 4.4 10.1 - - - -
159A TRP* 1.3 81.7 - - - +
161A LYS* 1.3 59.8 + - - +
162A ASP 4.2 0.4 - - - -
163A PHE* 3.7 15.0 - - - -
164A LEU 3.2 21.8 - - - +
165A PRO* 3.7 26.0 - - + -
166A VAL* 4.1 1.8 - - - -
198A LYS 3.7 0.4 - - - +
199A TYR* 3.3 7.1 - - - +
200A GLU* 2.8 53.3 + - + +
202A VAL* 3.5 23.6 - - + -
211A TYR* 3.9 16.4 - + - -
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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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160A PHE* 1.3 73.2 - - - +
162A ASP* 1.3 99.9 + - - +
163A PHE 3.2 0.2 - - - -
164A LEU* 2.8 25.4 + - - +
166A VAL* 3.6 20.5 - - + +
175A ILE* 6.5 0.9 - - + -
194A SER 3.4 22.1 + - - -
195A ASP* 3.6 13.9 - - - +
196A GLN 2.8 22.2 + - - -
198A LYS 3.3 5.2 - - - +
199A TYR* 3.6 25.8 - - + +
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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