Contacts of the strand formed by residues 161 - 172 (chain A) in PDB entry 2CMG
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LYS* 4.3 5.1 - - - +
140A TYR 3.7 13.7 - - - +
141A ASP 3.9 3.1 - - - +
143A ILE* 3.7 23.8 - - + -
157A LEU 3.6 1.5 + - - +
158A LYS* 3.4 10.1 + - - +
159A ARG 5.1 0.9 - - - -
160A MET* 1.3 79.3 + - - +
162A LYS* 1.3 65.3 + - - +
165A GLY* 3.7 11.4 - - - +
166A VAL* 3.3 48.7 - - - +
167A PHE* 3.9 7.9 - - + +
192A PHE* 4.1 17.3 - - + -
213A ALA 4.7 1.1 - - - +
214A SER* 4.8 1.1 - - - -
215A PHE* 3.7 29.9 - - + -
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Residues in contact with LYS 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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74A LYS* 5.3 4.0 - - - +
75A GLU* 4.8 8.0 - - - +
139A LYS* 3.5 39.5 - - + -
140A TYR 3.0 18.2 + - - +
141A ASP* 3.0 38.0 + - - +
161A LEU* 1.3 80.2 - - - +
163A GLU* 1.3 83.4 + - - +
164A ASP* 3.4 6.5 - - - +
165A GLY* 3.1 15.9 + - - +
215A PHE* 3.3 11.6 - - - -
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Residues in contact with GLU 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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139A LYS* 6.0 1.2 - - - +
162A LYS* 1.3 92.8 - - - +
164A ASP* 1.3 63.4 + - + +
165A GLY 3.5 1.0 + - - +
215A PHE* 3.6 24.8 + - - +
216A LYS* 4.7 5.7 + - - +
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Residues in contact with ASP 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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70A LYS* 2.8 40.9 + - + +
141A ASP* 4.8 1.7 - - - +
162A LYS* 4.3 9.7 - - - +
163A GLU* 1.3 77.5 + - + +
165A GLY* 1.3 64.9 + - - +
216A LYS* 2.9 30.5 - - - +
217A THR* 2.7 19.5 + - - +
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Residues in contact with GLY 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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70A LYS* 3.8 5.2 - - - -
141A ASP 3.4 14.1 - - - -
161A LEU* 3.7 15.4 - - - +
162A LYS* 3.1 22.0 + - - +
164A ASP* 1.3 86.6 + - - +
166A VAL* 1.3 63.4 + - - +
214A SER* 3.6 15.8 - - - -
215A PHE 4.5 2.9 + - - -
217A THR* 4.1 0.3 + - - -
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Residues in contact with VAL 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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66A GLY* 5.1 0.4 - - - -
69A THR* 4.8 3.8 - - + -
70A LYS* 4.3 9.4 - - + -
141A ASP 3.0 6.9 + - - -
142A LEU* 3.5 17.3 - - + +
143A ILE 3.1 23.2 + - - -
161A LEU* 3.3 9.1 - - - +
164A ASP 4.1 2.0 - - - +
165A GLY* 1.3 79.8 - - - +
167A PHE* 1.3 63.7 + - - +
168A ILE* 3.2 25.8 - - + -
212A TYR* 3.4 24.5 - - + +
213A ALA 3.5 11.4 - - - +
214A SER* 4.5 1.3 - - - -
217A THR* 3.4 31.2 - - + -
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Residues in contact with PHE 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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143A ILE* 3.0 46.2 - - + -
145A CYS* 3.7 25.1 - - + -
149A PRO* 4.7 8.1 - - + -
154A ILE* 5.0 8.5 - - + -
157A LEU* 3.6 27.4 - - + -
158A LYS* 5.9 0.7 - - - -
161A LEU* 3.9 13.0 - - + +
166A VAL* 1.3 72.7 - - - +
168A ILE* 1.3 63.7 + - - +
169A SER* 4.3 2.9 - - - -
188A MET* 3.2 36.5 - - + +
192A PHE* 3.7 22.9 - + + -
211A ILE 3.6 2.1 - - - +
213A ALA* 2.7 44.1 + - + +
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Residues in contact with ILE 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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62A LEU* 4.0 12.8 - - + +
65A MET* 4.2 8.3 - - + -
66A GLY* 4.3 8.1 - - - +
142A LEU* 4.2 16.4 - - + -
143A ILE 3.1 9.8 + - - +
144A PHE* 3.4 29.5 - - + -
145A CYS 3.1 21.5 + - - -
166A VAL* 3.2 35.2 - - + -
167A PHE* 1.3 73.4 - - - +
169A SER* 1.3 69.0 + - - +
198A PHE* 3.9 22.7 - - + -
211A ILE 3.3 5.2 - - - +
212A TYR* 3.7 25.4 - - + -
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Residues in contact with SER 169 (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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145A CYS* 3.5 23.1 - - - -
149A PRO* 4.2 14.4 - - - +
167A PHE* 4.3 2.7 - - - -
168A ILE* 1.3 77.6 - - - +
170A VAL* 1.3 63.3 + - - +
188A MET* 3.0 30.2 - - - +
210A TYR* 3.2 8.2 - - - +
211A ILE* 2.7 44.4 + - - +
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Residues in contact with VAL 170 (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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48A GLN* 5.8 2.5 - - - +
58A GLU* 5.2 0.2 - - - +
62A LEU* 5.4 5.8 - - + -
145A CYS 3.4 14.8 + - - +
146A LEU* 3.9 17.5 - - + +
147A GLN* 4.2 10.4 + - - -
148A GLU* 3.3 27.3 - - + +
149A PRO* 4.2 3.1 - - - +
169A SER* 1.3 80.6 + - - +
171A ALA* 1.3 82.7 + - - +
208A LYS* 3.6 35.7 - - + +
209A GLY 3.3 12.6 - - - +
210A TYR* 4.0 12.1 - - + -
211A ILE* 5.1 2.4 - - - +
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Residues in contact with ALA 171 (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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148A GLU* 4.1 13.0 - - - +
170A VAL* 1.3 84.8 - - - +
172A LYS* 1.3 68.9 + - - +
180A SER* 5.7 0.2 - - - +
181A MET* 4.0 29.4 - - + -
184A ALA* 4.1 11.2 - - + -
207A ASN 4.7 0.2 - - - +
208A LYS* 4.0 4.2 - - - +
209A GLY 2.9 21.7 + - - +
211A ILE* 4.1 14.8 - - + -
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Residues in contact with LYS 172 (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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148A GLU* 4.3 10.0 + - - +
171A ALA* 1.3 82.5 - - - +
173A HIS* 1.3 64.4 + - - +
174A PRO* 3.3 3.1 - - - +
177A GLU* 3.1 40.2 + - + +
180A SER* 3.1 31.5 + - - +
181A MET* 3.5 22.0 - - - +
207A ASN* 4.2 15.5 - - - +
209A GLY* 3.7 5.2 - - - +
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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