Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 2AQ5
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 VAL 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A TRP* 3.8 7.7 - - - -
140A HIS* 2.9 55.1 + - + +
143A ALA* 3.3 18.2 + - + +
144A GLN 3.1 12.9 + - - +
145A ASN* 1.3 76.7 - - - +
147A LEU* 1.3 61.9 + - - +
158A VAL* 3.5 27.6 - - + -
159A TRP 3.4 6.3 - - - +
160A ASP* 5.4 0.9 - - + -
167A VAL* 6.0 0.9 - - + -
184A TRP* 4.6 2.5 - - + -
376A ALA* 3.8 21.1 - - + +
379A TRP* 4.1 14.4 - - + -
380A LEU* 5.5 3.1 - - + -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 3.8 24.5 - - + -
106A VAL* 3.9 9.9 - - + -
108A VAL* 4.1 4.0 - - + -
127A LEU* 3.9 24.5 - - + -
137A VAL* 4.5 3.1 - - + -
138A ALA 3.7 24.5 - - - +
139A TRP* 3.8 25.4 - - + +
140A HIS 4.5 0.2 - - - +
146A VAL* 1.3 76.4 - - - +
148A LEU* 1.3 73.7 + - - +
149A SER* 5.8 0.2 - - - -
158A VAL* 3.4 4.1 - - - -
159A TRP* 2.8 44.8 + - + +
161A VAL* 3.8 21.8 - - + -
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 4.7 3.4 - - + -
137A VAL* 3.4 3.1 - - - -
138A ALA* 2.9 48.5 + - + +
147A LEU* 1.3 77.8 - - - +
149A SER* 1.3 76.5 + - - +
150A ALA* 4.2 2.7 - - + +
156A ILE* 3.6 26.9 - - + -
157A LEU 3.4 4.5 - - - +
158A VAL* 4.3 9.0 - - + +
182A VAL* 3.8 39.9 - - + -
184A TRP* 3.8 27.9 - - + +
191A ILE* 4.0 14.6 - - + -
205A PRO* 5.9 0.2 - - + -
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.8 24.4 - - - +
130A HIS* 2.8 26.9 + - - -
134A VAL* 4.0 2.0 - - - -
136A ILE 3.3 11.2 - - - -
137A VAL* 4.4 1.3 - - - -
147A LEU* 4.2 0.6 + - - -
148A LEU* 1.3 78.1 - - - +
150A ALA* 1.3 60.8 + - - +
156A ILE* 3.3 6.1 - - - +
157A LEU 2.9 33.2 + - - +
159A TRP* 2.9 25.6 + - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A HIS* 4.0 2.2 - - - -
134A VAL* 3.7 2.3 - - - +
135A GLY 3.5 5.4 + - - -
136A ILE* 3.0 48.8 + - + +
148A LEU* 4.2 0.4 - - + +
149A SER* 1.3 75.0 - - - +
151A GLY* 1.3 59.6 + - - +
155A VAL 3.4 5.8 - - - +
156A ILE* 4.0 19.1 - - + -
179A ILE* 4.1 12.3 - - + -
182A VAL* 4.2 13.2 - - + -
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Residues in contact with GLY 151 (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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130A HIS* 3.4 9.5 - - - -
132A LYS 4.7 0.2 - - - -
133A ARG 3.3 11.9 - - - -
134A VAL* 4.1 4.0 - - - -
135A GLY 4.7 0.4 - - - -
150A ALA* 1.3 75.4 - - - +
152A CSO 1.3 60.0 + - - -
153A ASP* 3.1 15.0 - - - -
154A ASN* 2.9 22.5 + - - +
155A VAL 3.2 10.1 + - - +
179A ILE* 4.5 7.4 + - - +
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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