Contacts of the strand formed by residues 159 - 163 (chain A) in PDB entry 1AVU
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 ARG 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.0 13.9 - - - +
26A PHE* 3.8 39.8 - - - -
44A VAL* 3.5 5.3 - - - +
45A GLN* 2.7 74.7 + - - +
47A ARG* 4.5 11.3 - - + +
150A ILE* 3.5 35.7 - - + +
151A SER 3.5 4.7 - - - -
152A ILE* 3.2 28.3 - - + +
157A GLY 4.0 6.3 - - - +
158A THR* 1.3 69.4 - - - +
160A ARG* 1.3 60.8 + - - +
161A LEU 4.0 0.5 + - - -
169A LEU* 4.9 0.2 - - - +
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Residues in contact with ARG 160 (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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34A THR* 4.4 20.2 - - - +
42A THR* 3.7 24.7 - - + -
43A VAL 3.8 3.6 - - - -
44A VAL* 4.4 4.9 - - + -
101A GLU* 3.8 37.2 + - - +
150A ILE* 3.4 1.2 - - - -
151A SER* 2.6 87.7 + - - +
152A ILE 3.5 11.3 + - - -
153A ASP* 3.5 35.7 + - - +
158A THR* 3.4 2.7 + - - -
159A ARG* 1.3 74.0 - - - +
161A LEU* 1.3 66.5 + - - +
162A VAL* 3.4 6.6 + - + -
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Residues in contact with LEU 161 (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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29A ILE* 4.0 20.0 - - + -
42A THR* 5.6 0.3 - - - +
43A VAL* 3.1 32.1 + - + +
44A VAL 4.2 0.9 - - - -
45A GLN 3.9 23.3 - - - +
93A TRP* 4.0 20.2 - - + -
104A ALA* 4.0 1.4 - - - +
105A VAL* 3.2 34.1 + - + +
133A LEU* 5.1 3.4 - - + -
148A ILE* 3.9 24.5 - - + -
149A GLY 3.4 8.1 - - - +
150A ILE* 4.0 15.3 - - + -
160A ARG* 1.3 71.2 - - - +
162A VAL* 1.3 63.0 + - - +
169A LEU* 4.1 9.4 - - + -
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Residues in contact with VAL 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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101A GLU* 3.6 34.8 - - + +
102A GLY* 4.8 1.1 - - - -
103A PRO 3.3 11.7 - - - +
104A ALA* 4.3 10.5 - - + +
105A VAL* 4.5 1.3 - - - +
148A ILE* 3.5 5.8 - - - -
149A GLY 2.9 27.3 + - - -
150A ILE 4.6 3.8 - - - +
151A SER* 3.7 31.4 - - - +
160A ARG* 3.4 8.0 + - + +
161A LEU* 1.3 79.7 - - - +
163A VAL* 1.3 68.4 + - - +
164A SER* 3.2 9.6 + - - +
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Residues in contact with VAL 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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95A VAL* 3.9 19.5 - - + -
102A GLY* 5.4 0.9 - - - -
103A PRO* 2.8 48.5 + - + +
105A VAL* 5.2 1.3 - - + -
114A MET* 5.5 1.1 - - + -
135A PHE* 4.5 8.1 - - + +
146A GLY* 3.6 34.8 - - - +
147A ASP 3.5 3.1 - - - -
148A ILE* 3.6 19.5 - - + -
162A VAL* 1.3 74.1 - - - +
164A SER* 1.3 61.2 + - - +
165A LYS 4.3 1.1 + - - +
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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