Contacts of the strand formed by residues 173 - 182 (chain A) in PDB entry 3AB0
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ILE* 4.9 3.4 - - + -
140A ALA 3.1 9.0 - - - +
141A ASN* 3.4 25.4 - - - +
167A LEU* 4.8 1.6 - - - +
171A GLY 4.6 1.1 - - - +
172A ALA* 1.3 96.1 - - + +
174A ILE* 1.3 61.5 + - - +
175A VAL* 4.0 19.5 + - + +
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Residues in contact with ILE 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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138A VAL* 3.8 1.7 - - - +
139A ILE* 3.5 1.6 - - - -
140A ALA* 2.7 43.6 + - + +
142A THR* 3.8 20.9 - - + -
149A GLY 4.6 1.1 - - - +
150A GLY* 4.9 0.2 - - - -
151A LEU* 4.4 12.3 - - + +
165A SER* 3.8 35.7 - - - +
166A SER 4.9 1.6 - - - +
167A LEU* 3.7 43.3 - - + +
173A PRO* 1.3 74.5 - - - +
175A VAL* 1.3 61.5 + - - +
176A ILE* 4.1 13.1 + - + +
198A LEU* 3.9 16.4 - - + -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR* 6.5 0.7 - - - -
138A VAL 3.4 3.1 - - - +
139A ILE* 3.7 30.7 - - + -
165A SER* 4.5 5.6 + - - -
173A PRO* 4.0 23.2 + - + +
174A ILE* 1.3 76.2 - - - +
176A ILE* 1.3 67.1 + - - +
177A GLN* 4.4 2.1 + - + -
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Residues in contact with ILE 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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136A ILE 4.0 1.0 - - - +
137A THR* 3.3 2.6 - - - -
138A VAL* 2.7 58.1 + - + +
151A LEU* 3.9 34.5 - - + -
152A THR* 4.3 3.6 - - - +
153A ILE* 3.7 14.4 - - + -
162A GLY 5.0 0.9 - - - +
163A THR* 3.7 46.2 - - + +
165A SER* 3.4 21.3 - - - +
174A ILE* 4.2 8.3 - - + +
175A VAL* 1.3 78.6 - - - +
177A GLN* 1.3 65.1 + - - +
191A VAL* 4.7 2.5 - - + -
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Residues in contact with GLN 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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135A LYS* 5.0 8.4 - - - -
136A ILE 3.5 6.3 - - - -
137A THR* 3.9 19.0 - - + +
162A GLY 4.5 8.1 - - - +
175A VAL* 4.4 2.2 + - + +
176A ILE* 1.3 81.3 - - - +
178A ALA* 1.3 64.9 + - - +
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Residues in contact with ALA 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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134A TYR 3.7 0.7 - - - +
135A LYS* 3.5 4.2 - - - +
136A ILE* 2.8 42.5 + - + +
137A THR* 5.0 0.6 - - - +
153A ILE* 4.5 3.8 - - + -
160A VAL* 3.9 17.0 - - + -
161A PRO 5.2 3.1 - - - +
162A GLY 5.4 0.4 - - - +
163A THR* 3.7 25.1 - - + -
177A GLN* 1.3 78.5 - - - +
179A ILE* 1.3 62.0 + - - +
180A THR* 5.3 1.1 - - + +
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Residues in contact with ILE 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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133A PHE* 4.6 21.5 - - + -
134A TYR 3.3 7.2 - - - +
135A LYS* 4.1 25.6 - - + -
160A VAL* 4.8 3.3 - - - +
178A ALA* 1.3 78.5 - - - +
180A THR* 1.3 69.7 + - - +
213A VAL* 5.1 7.9 - - + -
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Residues in contact with THR 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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133A PHE* 4.5 0.2 - - - -
134A TYR* 2.9 37.4 + - + +
136A ILE* 4.0 18.6 - - + -
155A VAL* 4.0 29.5 - - + +
160A VAL* 4.2 18.8 - - + +
178A ALA 5.3 0.9 - - - +
179A ILE* 1.3 82.0 - - - +
181A GLN* 1.3 70.2 + - - +
182A ILE* 3.6 9.7 + - + +
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Residues in contact with GLN 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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132A GLY* 3.7 4.9 - - - +
133A PHE* 3.6 44.6 - - + +
179A ILE* 5.1 0.2 - - - +
180A THR* 1.3 79.3 + - - +
182A ILE* 1.3 66.4 + - - +
183A THR* 3.4 30.8 + - + +
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Residues in contact with ILE 182 (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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128A ILE* 3.9 18.8 - - + -
130A GLU 3.4 21.3 - - - +
131A THR* 3.4 7.4 - - - -
132A GLY* 2.7 39.7 + - - +
134A TYR* 3.6 24.7 - - + -
155A VAL* 3.6 39.0 - - + -
180A THR* 3.6 8.0 + - + +
181A GLN* 1.3 79.4 + - - +
183A THR* 1.3 64.3 + - - +
184A THR 4.1 7.2 - - - +
185A THR* 4.8 1.1 - - + -
187A SER* 3.4 24.9 - - - +
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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