Contacts of the strand formed by residues 184 - 193 (chain A) in PDB entry 3ABD
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 PRO 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A MET* 3.5 32.3 - - + +
182A HIS 3.6 0.2 - - - -
183A ASP* 1.3 95.8 - - - +
185A ARG* 1.3 60.1 + - - +
186A LEU* 4.0 1.0 + - + -
204A GLU* 4.1 23.8 - - + +
205A GLU 3.5 7.0 - - - +
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Residues in contact with ARG 185 (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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136A VAL 5.8 1.3 - - - -
138A ASP* 4.2 14.0 + - - -
183A ASP 5.0 1.1 - - - +
184A PRO* 1.3 75.2 - - - +
186A LEU* 1.3 61.3 + - - +
187A ILE* 3.7 19.8 + - + +
203A VAL 3.4 2.3 - - - +
204A GLU* 3.2 4.6 - - - -
205A GLU* 2.9 69.4 + - - +
206A ARG 3.9 1.4 + - - -
207A ALA* 3.8 36.7 + - + +
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Residues in contact with LEU 186 (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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184A PRO 4.0 1.6 + - - -
185A ARG* 1.3 75.7 - - - +
187A ILE* 1.3 67.4 + - - +
188A PRO* 3.6 30.1 - - + +
200A GLN* 5.8 2.2 - - - +
202A TYR* 3.1 49.4 - - + -
203A VAL 3.5 2.5 - - - +
204A GLU* 4.5 12.3 - - + +
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Residues in contact with ILE 187 (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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136A VAL* 3.7 38.1 - - + +
137A LEU* 3.7 28.5 - - + -
185A ARG* 3.8 31.6 - - + +
186A LEU* 1.3 79.6 - - - +
188A PRO* 1.3 74.9 - - + +
189A LEU* 3.5 8.4 + - + +
202A TYR* 3.5 0.2 - - - -
203A VAL* 2.8 42.0 + - + +
205A GLU* 4.1 9.2 - - + +
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Residues in contact with PRO 188 (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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129A LYS* 5.5 0.7 - - - -
186A LEU* 3.6 22.2 - - + +
187A ILE* 1.3 93.0 - - + +
189A LEU* 1.3 64.3 + - - +
190A LYS 5.5 0.2 - - - +
200A GLN* 5.3 8.5 - - - +
201A LEU 4.3 0.2 - - - +
202A TYR* 3.9 11.0 - - + -
112B SER* 3.9 22.3 - - - +
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Residues in contact with LEU 189 (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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98A PHE* 4.4 6.3 - - + -
129A LYS* 3.2 32.7 - - + +
130A ILE* 4.4 11.2 - - + +
133A CYS* 4.1 27.6 - - + -
136A VAL* 4.8 4.3 - - + -
187A ILE* 3.5 21.0 + - + +
188A PRO* 1.3 82.2 - - - +
190A LYS* 1.3 63.0 + - - +
201A LEU* 2.9 44.9 + - + +
203A VAL* 3.7 25.6 - - + +
112B SER* 3.2 20.9 - - - -
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Residues in contact with LYS 190 (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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125A ALA* 3.6 27.1 - - + -
126A PHE* 3.5 47.0 - - + +
129A LYS* 4.3 2.9 - - + -
189A LEU* 1.3 81.5 - - + +
191A THR* 1.3 71.6 + - - +
192A MET* 6.0 0.4 - - - -
200A GLN* 3.5 1.4 - - - +
201A LEU* 2.8 36.6 + - - +
110B ILE* 4.2 9.8 - - + +
111B SER* 3.0 24.1 + - - +
112B SER 3.3 6.0 + - - +
113B ASP 2.6 26.5 + - - -
115B LEU* 4.0 15.6 - - - +
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Residues in contact with THR 191 (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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126A PHE* 4.0 2.9 - - - -
190A LYS* 1.3 83.6 - - - +
192A MET* 1.3 70.8 + - - +
193A THR* 5.0 2.7 - - - +
199A MET 3.3 12.1 - - - +
200A GLN* 3.3 29.4 + - + +
112B SER 3.3 8.8 + - - -
113B ASP* 5.4 0.3 - - - -
114B SER* 3.4 40.5 - - - -
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Residues in contact with MET 192 (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* 4.3 10.8 - - + -
122A LEU* 3.9 40.6 - - + +
123A LEU* 3.6 27.6 - - - -
126A PHE* 3.7 23.5 - - + -
190A LYS* 6.0 0.9 - - - -
191A THR* 1.3 80.8 - - - +
193A THR* 1.3 65.3 + - - +
194A SER* 3.9 12.8 - - - +
197A LEU* 3.8 34.3 - - + +
198A LYS* 3.4 3.6 - - - +
199A MET* 2.8 41.9 + - + +
114B SER* 4.4 2.9 - - - -
116B LEU* 6.3 0.2 - - - -
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Residues in contact with THR 193 (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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122A LEU* 3.8 7.3 - - - +
191A THR* 5.0 3.1 - - - +
192A MET* 1.3 78.7 + - - +
194A SER* 1.3 69.5 + - - +
197A LEU 3.7 3.1 - - - -
198A LYS* 3.3 29.5 - - + +
114B SER* 4.2 14.8 + - - -
116B LEU* 3.2 30.9 - - + +
117B SER* 5.5 4.3 - - - -
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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