Contacts of the helix formed by residues 2148 - 2153 (chain B) in PDB entry 1V9P
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 VAL2148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2071B PRO* 4.1 6.1 - - + -
2073B PHE* 4.4 15.0 - - + -
2124B VAL* 5.3 0.9 - - + -
2136B GLY 2.8 18.3 + - - +
2137B ALA 4.3 1.3 - - - -
2138B THR* 3.4 31.2 - - + +
2146B GLU 3.6 3.1 - - - +
2147B GLU* 1.3 74.6 - - - +
2149B THR* 1.3 66.1 + - - +
2150B GLN 3.7 0.9 - - - -
2151B ASN* 3.4 30.3 + - + +
2152B LEU* 3.4 13.0 + - + +
2208B LEU* 3.5 33.0 - - + +
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Residues in contact with THR2149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2018B ARG* 3.8 27.3 + - - +
2058B ASP* 5.8 1.1 - - - +
2133B LEU* 5.6 8.1 - - + -
2134B VAL 4.2 0.4 + - - -
2135B PHE* 3.1 13.2 - - - +
2136B GLY 2.7 30.6 + - - +
2147B GLU* 2.5 21.2 + - - -
2148B VAL* 1.3 71.1 - - - +
2150B GLN* 1.3 70.8 + - + +
2152B LEU* 2.8 23.0 + - + +
2153B LEU* 3.2 23.9 + - + +
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Residues in contact with GLN2150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2018B ARG* 3.3 42.9 + - + +
2021B ASN* 4.3 3.6 - - - +
2022B TYR* 4.7 8.9 + - - +
2026B VAL* 6.1 1.0 - - - +
2063B GLN* 6.3 0.2 - - - +
2069B LEU* 3.7 39.2 - - + +
2070B GLU 4.8 3.4 - - - +
2071B PRO* 4.3 23.2 - - + +
2147B GLU* 4.3 1.2 + - - -
2148B VAL 3.7 0.4 - - - -
2149B THR* 1.3 81.7 - - + +
2151B ASN* 1.3 64.5 + - - +
2153B LEU* 3.5 21.9 + - - +
2154B THR* 3.8 10.2 - - - +
2213B PRO* 4.2 9.8 - - + +
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Residues in contact with ASN2151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2071B PRO* 3.6 11.5 - - - +
2148B VAL* 3.4 23.4 + - + +
2149B THR 2.8 3.4 + - - -
2150B GLN* 1.3 71.3 - - - +
2152B LEU* 1.3 65.3 + - - +
2154B THR* 2.7 29.4 + - - -
2155B ILE* 4.4 2.0 - - - +
2208B LEU* 2.3 34.2 - - + +
2210B GLN 3.3 25.0 + - - +
2213B PRO* 3.5 29.1 - - - +
2216B THR* 3.3 17.5 + - + +
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Residues in contact with LEU2152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2124B VAL* 4.3 14.6 - - + -
2126B LEU* 3.7 17.7 - - + -
2133B LEU* 6.0 4.3 - - + -
2136B GLY* 3.5 39.9 - - - +
2148B VAL* 3.5 13.5 - - + +
2149B THR* 2.8 12.3 + - + +
2151B ASN* 1.3 74.8 - - - +
2153B LEU* 1.3 60.1 + - + +
2155B ILE* 2.8 38.1 + - + +
2158B ILE* 3.9 20.1 - - + +
2175B VAL* 3.5 31.6 - - + -
2208B LEU* 4.2 11.2 - - + -
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Residues in contact with LEU2153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2015B ASP* 4.9 2.7 - - - +
2018B ARG* 4.0 28.0 - - + -
2019B TYR* 4.7 7.9 - - + +
2022B TYR* 3.9 23.1 + - + -
2133B LEU* 4.6 15.3 - - + -
2149B THR* 3.2 21.4 + - + +
2150B GLN* 3.6 22.7 - - - +
2151B ASN 3.1 0.8 - - - -
2152B LEU* 1.3 79.7 - - + +
2154B THR* 1.3 58.9 + - - +
2155B ILE 3.0 10.4 + - - +
2156B PRO* 4.8 0.7 - - - +
2158B ILE* 5.3 9.9 - - + +
2160B ARG* 3.5 40.6 - - + -
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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