Contacts of the strand formed by residues 167 - 171 (chain A) in PDB entry 5ABT
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 HIS 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ARG* 3.7 30.1 + - - -
121A ALA 3.5 22.7 - - - -
122A GLN* 3.3 38.5 + - - -
124A LEU 3.7 14.0 + - - +
125A VAL* 3.6 14.9 - - + -
126A LEU 3.0 21.3 + - - -
165A LEU* 3.6 5.9 - - - +
166A LYS* 1.3 95.3 - - + +
168A VAL* 1.3 65.7 + - - +
198A ALA* 3.6 19.4 + - + +
200A GLN* 4.8 6.4 + - - +
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Residues in contact with VAL 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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125A VAL* 4.2 2.9 - - - -
126A LEU* 3.2 15.5 - - + +
128A LEU* 3.9 23.6 - - + -
153A LEU* 5.5 0.4 - - + -
157A VAL* 4.8 0.9 - - + -
165A LEU* 3.9 25.1 - - + -
167A HIS* 1.3 78.7 - - - +
169A LEU* 1.3 70.8 + - - +
170A CYS* 4.0 2.8 + - + +
197A ILE* 3.6 26.2 - - + +
198A ALA 3.1 7.3 + - - +
199A PHE* 3.3 26.0 - - + -
200A GLN* 2.8 27.8 + - - +
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Residues in contact with LEU 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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47A HIS* 3.5 27.6 - - + +
77A GLN* 4.1 2.0 - - - +
100A VAL* 4.1 12.3 - - + -
125A VAL* 3.8 12.9 - - + +
126A LEU 2.9 7.3 + - - +
127A ALA* 3.3 6.3 - - + -
128A LEU 2.8 27.2 + - - -
129A ASP* 3.5 8.3 - - - +
168A VAL* 1.3 74.4 - - - +
170A CYS* 1.3 60.2 + - - +
171A THR* 3.4 24.9 - - - +
200A GLN* 3.7 14.1 - - + +
202A SER* 3.8 10.8 - - - +
223A ILE* 3.5 29.6 - - + -
1247A GUO 4.3 9.9 - - - +
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Residues in contact with CYS 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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128A LEU 3.4 10.5 - - - +
130A VAL* 4.4 5.8 - - - -
153A LEU* 3.6 31.2 - - + -
168A VAL* 4.0 8.7 - - + -
169A LEU* 1.3 74.5 - - - +
171A THR* 1.3 53.5 + - - +
186A LEU* 3.7 29.2 - - - -
187A TYR* 2.6 40.7 + - + -
190A VAL* 5.4 1.8 - - - -
199A PHE* 4.6 8.7 - - + -
200A GLN 3.1 9.0 + - - +
202A SER* 3.3 8.7 + - - -
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Residues in contact with THR 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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128A LEU 3.8 0.6 + - - -
129A ASP* 2.7 32.4 + - - -
130A VAL* 2.9 32.5 + - - +
145A TRP* 3.8 24.9 - - + -
169A LEU* 3.4 5.2 - - - +
170A CYS* 1.3 74.7 - - - +
172A ASP* 1.3 74.0 + - - +
173A ILE 3.4 1.5 + - - +
176A ALA* 3.9 10.1 - - + -
202A SER* 2.7 36.7 + - - +
203A GLY* 4.1 0.7 - - - -
1247A GUO 4.0 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