Contacts of the strand formed by residues 173 - 181 (chain A) in PDB entry 2DNH
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 SER 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LEU* 5.4 1.0 - - - +
142A ASN 4.2 6.8 + - - -
143A LYS* 4.5 28.2 - - - +
165A VAL* 3.9 15.9 - - - +
166A LEU 3.7 16.1 + - - -
167A ARG* 4.3 12.5 - - - +
171A GLY 4.2 1.4 + - - -
172A SER* 1.3 75.2 - - - +
174A LYS* 1.3 59.7 + - - +
175A GLY* 3.1 17.9 + - - -
176A CYS 4.3 0.2 + - - -
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Residues in contact with LYS 174 (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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166A LEU* 3.5 23.1 + - + +
167A ARG* 3.6 29.6 - - - +
168A GLY* 3.9 11.5 - - - -
169A PRO* 5.2 4.0 - - - +
172A SER 4.2 4.5 - - - +
173A SER* 1.3 72.2 + - - +
175A GLY* 1.3 58.7 + - - +
176A CYS* 3.1 24.1 - - - +
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Residues in contact with GLY 175 (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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139A GLY 2.9 2.4 - - - -
140A MET* 2.8 14.7 + - - -
141A LEU* 2.7 59.4 + - - +
173A SER* 3.1 13.1 + - - -
174A LYS* 1.3 78.0 - - - +
176A CYS* 1.3 56.7 + - - +
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Residues in contact with CYS 176 (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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137A PHE* 4.0 21.5 - - + -
138A VAL 2.9 16.6 - - - +
139A GLY* 4.0 8.7 - - - -
140A MET 4.7 1.3 - - - -
141A LEU* 4.1 3.4 - - - -
165A VAL* 3.5 8.3 - - - +
166A LEU* 3.0 37.4 + - + +
173A SER* 4.3 0.4 + - - -
174A LYS* 3.1 25.5 - - - +
175A GLY* 1.3 83.6 - - - +
177A ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 177 (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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137A PHE* 3.7 3.7 - - - -
138A VAL* 2.8 39.4 + - + +
141A LEU* 4.1 13.9 - - + +
150A VAL* 5.7 6.1 - - + -
163A CYS* 5.3 2.2 - - - -
164A THR 3.0 18.6 - - - +
165A VAL* 3.7 18.2 - - + +
166A LEU* 4.1 3.6 - - - +
176A CYS* 1.3 76.9 - - - +
178A PHE* 1.3 64.3 + - - +
179A VAL* 4.1 6.1 - - + -
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Residues in contact with PHE 178 (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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135A LYS* 3.4 33.4 - - + -
136A LEU 3.2 14.6 - - - -
137A PHE* 3.6 25.4 - + + -
162A GLU 4.0 0.9 - - - +
163A CYS* 3.4 3.5 - - - -
164A THR* 2.7 49.7 + - + +
166A LEU* 3.7 40.2 - - + -
177A ALA* 1.3 71.7 - - - +
179A VAL* 1.3 63.8 + - - +
180A LYS 4.2 0.2 - - - -
212A ALA* 3.6 24.9 - - + -
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Residues in contact with VAL 179 (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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135A LYS* 4.3 0.2 - - - -
136A LEU* 2.6 50.4 + - + +
138A VAL* 4.1 12.3 - - + -
150A VAL* 3.9 13.2 - - + -
151A LEU* 4.9 0.2 - - + -
154A PHE* 3.5 41.5 - - + -
160A ILE* 3.6 27.8 - - + -
162A GLU 3.9 1.8 - - - +
163A CYS* 4.2 12.1 - - + +
177A ALA* 4.9 3.1 - - + -
178A PHE* 1.3 79.0 - - - +
180A LYS* 1.3 60.0 + - - +
181A PHE* 4.1 7.2 - - + -
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Residues in contact with LYS 180 (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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134A ARG* 2.9 43.7 - - - +
135A LYS* 4.1 14.8 - - + +
160A ILE* 2.8 13.5 - - - +
161A ASP* 2.7 65.3 + - + -
162A GLU* 2.9 29.9 + - + +
178A PHE 4.2 0.4 - - - -
179A VAL* 1.3 74.5 - - - +
181A PHE* 1.3 57.2 + - - +
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Residues in contact with PHE 181 (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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134A ARG* 3.0 23.6 + - - +
136A LEU* 3.2 36.1 - - + -
154A PHE* 3.9 17.3 - + + -
158A GLY* 3.5 30.5 - - - -
159A VAL 4.2 0.9 - - - -
160A ILE* 3.2 30.5 - - + -
161A ASP* 3.3 12.6 - - - +
179A VAL* 4.1 7.2 - - + -
180A LYS* 1.3 77.7 - - - +
182A SER* 1.3 65.1 + - - +
183A SER 3.2 18.6 + - - +
186A GLU* 4.0 11.0 - - + -
187A ALA* 3.3 15.0 - - + +
190A ALA* 3.3 29.8 - - + -
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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