Contacts of the helix formed by residues 134 - 138 (chain B) in PDB entry 3V81
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 SER 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A VAL 4.9 0.2 - - - +
31B ILE* 4.0 5.4 - - - -
133B PRO* 1.3 78.0 - - - +
135B ILE* 1.3 68.2 + - - +
136B ASN 3.3 1.0 + - - -
137B ASN* 3.2 16.2 + - - +
138B GLU* 3.1 13.6 + - - -
139B THR* 2.6 47.3 + - - -
140B PRO 4.8 3.2 + - - -
141B GLY* 5.3 1.0 - - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY 6.1 0.2 - - - +
380A ILE 5.5 0.7 - - - -
381A VAL 4.3 1.8 - - - +
382A ILE 3.4 18.4 - - - +
383A TRP* 3.7 19.3 - - - +
384A GLY* 3.8 8.1 - - - +
26B LEU 5.1 2.0 - - - +
28B GLU* 3.0 52.7 - - + +
31B ILE* 3.7 20.2 - - + +
32B LYS* 4.8 6.5 - - - +
134B SER* 1.3 73.4 + - - +
136B ASN* 1.3 67.2 - - + +
137B ASN 2.8 7.3 + - - -
138B GLU* 3.3 22.5 + - - +
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Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 2.9 28.0 - - - +
96A HIS* 2.7 46.4 + - - +
99A GLY* 3.4 15.9 - - - +
100A LEU* 3.7 2.4 - - - +
381A VAL* 2.9 26.0 + - - +
382A ILE* 3.1 25.9 - - - +
134B SER 3.3 1.6 + - - -
135B ILE* 1.3 74.6 - - + +
137B ASN* 1.3 61.9 + - - +
138B GLU* 3.1 23.4 + - - +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.8 23.8 + - - +
93A GLY* 3.4 33.3 - - - +
94A ILE 3.7 7.9 + - - +
95A PRO* 3.7 21.5 - - - +
181A TYR* 3.8 6.4 - - - -
381A VAL* 5.2 11.8 - - - +
134B SER* 3.2 21.3 + - - +
135B ILE 2.8 4.9 + - - -
136B ASN* 1.3 80.6 - - - +
138B GLU* 1.3 61.2 + - - +
139B THR 3.5 5.1 + - - +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 4.8 3.1 - - + -
99A GLY 3.6 3.8 - - - +
100A LEU* 3.6 17.4 - - + +
101A LYS* 3.0 31.9 + - - -
179A VAL* 6.2 3.4 - - + -
180A ILE 4.2 9.4 - - - +
181A TYR* 3.2 31.1 - - + +
182A GLN* 4.9 1.7 + - - +
901A NVP 5.2 7.9 - - + +
134B SER* 3.1 4.0 + - - -
135B ILE* 3.3 21.6 + - - +
136B ASN* 3.1 28.8 + - - +
137B ASN* 1.3 78.0 - - - +
139B THR* 1.3 62.0 + - - +
140B PRO* 4.8 1.2 - - - +
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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