Contacts of the helix formed by residues 2039 - 2048 (chain B) in PDB entry 2NVU
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 THR2039 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2025B GLU* 3.9 24.2 - - + +
2038B SER* 1.3 80.9 + - - +
2040B GLU* 1.3 70.8 + - - +
2041B SER 3.5 0.4 - - - -
2042B LEU* 4.0 8.4 + - - +
2043B GLN* 3.4 21.7 + - - +
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Residues in contact with GLU2040 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2038B SER* 2.6 13.1 + - - +
2039B THR* 1.3 87.5 + - - +
2041B SER* 1.3 53.0 + - - +
2042B LEU 3.2 0.2 - - - -
2043B GLN* 2.7 26.6 + - - +
2044B PHE* 2.7 34.5 + - - +
9C GLN* 4.5 3.8 - - - +
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Residues in contact with SER2041 (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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2024B LEU* 4.1 32.8 + - - +
2035B PHE* 5.4 2.9 - - - -
2036B GLU 4.6 4.7 + - - -
2038B SER* 3.8 18.1 + - - -
2040B GLU* 1.3 75.9 - - - +
2042B LEU* 1.3 65.0 + - - +
2044B PHE* 2.8 15.1 + - - +
2045B LEU* 2.9 15.6 + - - +
2312B THR* 5.2 4.7 + - - -
9C GLN* 3.4 31.0 + - - -
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Residues in contact with LEU2042 (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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2017B TRP* 3.7 37.7 - - + -
2020B VAL* 4.7 9.2 - - + -
2021B LYS* 3.8 27.6 - - + -
2024B LEU* 3.9 16.1 - - + +
2025B GLU* 5.5 2.7 - - + +
2038B SER 5.1 0.6 + - - +
2039B THR* 4.0 11.2 + - - +
2040B GLU 3.2 0.6 - - - -
2041B SER* 1.3 77.5 - - - +
2043B GLN* 1.3 64.1 + - - +
2045B LEU* 3.1 14.7 + - + -
2046B LEU* 2.7 53.8 + - + +
2071B GLY* 4.6 8.7 - - - -
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Residues in contact with GLN2043 (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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1180B LYS* 3.8 30.4 + - - +
2039B THR* 3.4 17.2 - - - +
2040B GLU* 2.7 31.6 + - - +
2042B LEU* 1.3 76.1 - - - +
2044B PHE* 1.3 53.2 + - - -
2046B LEU* 4.0 15.6 - - - +
2047B ASP* 2.6 63.7 + - - +
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Residues in contact with PHE2044 (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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2040B GLU 2.7 13.3 + - - +
2041B SER* 2.8 9.8 + - - +
2043B GLN* 1.3 72.9 - - - +
2045B LEU* 1.3 63.8 + - + +
2047B ASP* 5.2 0.2 - - - -
2048B THR* 2.9 50.7 + - - -
2049B CYS* 3.0 40.3 + - + -
2139B HIS* 4.2 10.5 - + - -
2311B ALA 3.4 22.7 - - - -
2312B THR* 5.9 0.4 - - + -
7C LEU* 3.9 17.3 - - + -
8C LYS 4.1 2.0 - - - -
9C GLN* 3.3 63.9 - - + +
10C GLN 3.9 3.6 - - - -
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Residues in contact with LEU2045 (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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2020B VAL* 4.6 2.2 - - + -
2024B LEU* 4.4 11.7 - - + -
2041B SER 2.9 12.6 + - - +
2042B LEU* 3.3 9.9 - - + +
2044B PHE* 1.3 83.9 - - + +
2046B LEU* 1.3 60.5 + - - +
2049B CYS* 4.2 14.3 + - + +
2070B SER 3.5 24.7 - - - +
2071B GLY* 3.2 19.4 - - - +
2072B PHE* 3.6 44.3 - - + -
2073B ARG 3.7 3.8 + - - -
2074B GLN* 4.9 1.2 + - - +
2308B PHE* 3.6 19.5 - - + -
2311B ALA* 3.9 14.6 - - + -
2312B THR* 3.9 16.6 - - + -
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Residues in contact with LEU2046 (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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1180B LYS* 5.2 0.7 - - - +
2012B ASP* 4.2 8.1 - - - +
2017B TRP* 3.7 31.2 - - + +
2042B LEU* 2.7 48.7 + - + +
2043B GLN* 4.0 19.5 - - - +
2045B LEU* 1.3 76.0 - - - +
2047B ASP* 1.3 65.0 + - - +
2071B GLY 3.4 13.2 - - - +
2073B ARG* 3.2 62.6 - - + +
2074B GLN* 3.5 11.9 + - - -
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Residues in contact with ASP2047 (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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1176B LYS* 4.0 24.1 + - - +
1179B ILE* 5.9 2.3 - - - +
2043B GLN* 2.6 47.7 + - - +
2046B LEU* 1.3 83.0 - - - +
2048B THR* 1.3 72.1 + - + +
2073B ARG* 4.6 6.4 + - - -
2074B GLN* 3.1 19.8 + - - +
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Residues in contact with THR2048 (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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1176B LYS* 6.2 0.2 - - - +
2044B PHE* 2.9 40.6 + - - -
2045B LEU 4.6 0.2 + - - -
2046B LEU 4.0 0.2 - - - -
2047B ASP* 1.3 89.6 - - + +
2049B CYS* 1.3 57.0 + - - +
2050B LYS* 2.8 19.6 + - - +
2074B GLN* 4.6 6.8 - - - +
2139B HIS* 3.7 8.2 + - - -
10C GLN* 5.3 0.3 - - - -
11C LYS* 4.7 26.5 + - + +
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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