Contacts of the helix formed by residues 2166 - 2183 (chain A) in PDB entry 4NF9
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 PRO2166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2164A GLN 3.6 6.3 - - - +
2165A ALA* 1.3 89.1 - - + +
2167A PRO* 1.3 77.0 - - + +
2168A SER* 3.4 2.7 - - - +
2169A SER* 3.3 4.7 + - - +
2170A LEU* 3.2 19.9 + - - +
2218A GLU* 4.0 12.6 - - - +
268C LYS 4.5 4.3 - - - +
269C TRP* 3.2 58.8 - - + +
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Residues in contact with PRO2167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2165A ALA 4.7 0.7 - - - +
2166A PRO* 1.3 86.2 - - + +
2168A SER* 1.3 60.4 + - - +
2170A LEU* 3.2 15.3 + - + +
2171A LEU* 2.8 28.8 + - - +
2218A GLU* 5.6 0.7 - - - +
2221A LYS* 5.0 13.0 - - + +
2234A ILE* 3.9 28.3 - - + +
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Residues in contact with SER2168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2166A PRO* 4.5 1.2 - - - +
2167A PRO* 1.3 78.9 - - - +
2169A SER* 1.3 75.4 + - - +
2171A LEU* 3.0 15.4 + - - +
2172A VAL* 3.0 19.3 + - - +
2214A GLY* 3.9 16.1 + - - -
2217A ILE* 3.9 26.5 - - - -
2218A GLU* 2.5 34.2 + - - +
2221A LYS* 5.5 1.7 - - - +
2234A ILE* 3.8 10.8 - - - +
269C TRP* 5.3 0.5 - - - +
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Residues in contact with SER2169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2160A LEU* 4.2 5.2 - - - -
2165A ALA* 4.4 6.7 - - - -
2166A PRO* 3.3 10.7 + - - +
2167A PRO 3.3 0.4 - - - -
2168A SER* 1.3 80.6 + - - +
2170A LEU* 1.3 56.9 + - - +
2172A VAL* 2.8 27.0 + - - +
2173A HIS* 3.1 15.6 + - - -
269C TRP* 2.5 45.1 + - - +
270C TYR* 3.6 24.5 - - - -
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Residues in contact with LEU2170 (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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2160A LEU* 4.0 7.9 - - + -
2162A GLU* 3.4 52.5 - - + +
2165A ALA* 3.9 22.0 - - + +
2166A PRO 3.2 14.0 + - - +
2167A PRO* 3.4 15.0 - - + +
2169A SER* 1.3 78.7 - - - +
2171A LEU* 1.3 56.5 + - - +
2173A HIS* 3.6 3.9 + - + +
2174A LYS* 2.9 26.0 + - - +
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Residues in contact with LEU2171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2167A PRO 2.8 15.8 + - - +
2168A SER* 3.0 8.9 + - - +
2170A LEU* 1.3 72.8 - - - +
2172A VAL* 1.3 60.5 + - + +
2174A LYS* 3.5 8.2 - - + +
2175A LEU* 2.9 45.9 + - + +
2213A LEU* 4.2 12.6 - - + -
2217A ILE* 3.8 28.5 - - + -
2234A ILE* 4.1 27.4 - - + -
2237A ASN* 4.2 24.2 - - - +
2238A GLU 6.3 0.2 - - - -
2258A LEU* 4.0 21.8 - - + -
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Residues in contact with VAL2172 (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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2124A VAL* 5.2 1.8 - - + -
2168A SER 3.1 16.2 - - - +
2169A SER 2.8 8.5 + - - +
2171A LEU* 1.3 80.2 - - + +
2173A HIS* 1.3 71.9 + - + +
2175A LEU* 3.1 3.3 + - - +
2176A ILE* 2.9 45.3 + - + +
2210A CYS* 3.6 34.5 - - - +
2211A ARG* 3.9 9.2 - - + -
2213A LEU* 5.7 1.8 - - + -
2214A GLY* 3.6 19.1 - - - -
270C TYR* 3.7 18.2 - - + +
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Residues in contact with HIS2173 (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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2124A VAL* 4.4 3.7 - - + +
2127A THR* 2.9 36.1 + - - -
2128A ILE* 3.8 19.1 - - + +
2158A SER* 2.6 32.3 + - - +
2160A LEU* 3.3 38.5 - - + +
2162A GLU* 6.6 0.4 - - - -
2169A SER 3.1 10.7 + - - +
2170A LEU* 4.0 5.6 - - + +
2172A VAL* 1.3 80.2 - - + +
2174A LYS* 1.3 64.8 + - - +
2176A ILE* 4.5 2.2 - - - +
2177A PHE* 3.2 36.8 + + + +
270C TYR* 4.6 9.9 - + - -
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Residues in contact with LYS2174 (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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2170A LEU 2.9 19.7 + - - +
2171A LEU* 3.2 13.8 + - + +
2173A HIS* 1.3 72.7 - - - +
2175A LEU* 1.3 63.2 + - - +
2177A PHE* 4.1 1.3 - - - +
2178A GLN* 3.1 48.4 + - + +
2236A ASN* 3.1 32.8 + - - +
2237A ASN* 3.1 31.9 - - - +
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Residues in contact with LEU2175 (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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2171A LEU* 2.9 33.0 + - + +
2172A VAL* 3.8 3.8 - - - +
2174A LYS* 1.3 75.6 - - - +
2176A ILE* 1.3 66.0 + - - +
2178A GLN* 3.4 10.3 + - - +
2179A TYR 3.3 14.7 + - - -
2210A CYS* 4.0 16.6 - - + -
2213A LEU* 3.7 28.5 - - + -
2237A ASN* 2.8 41.1 - - - +
2258A LEU* 4.0 5.8 - - + +
2259A SER 3.6 24.9 - - - +
2260A ALA* 3.4 15.6 - - - +
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Residues in contact with ILE2176 (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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2124A VAL* 4.2 7.6 - - + -
2128A ILE* 3.5 35.9 - - + -
2172A VAL* 2.9 39.4 + - + +
2173A HIS* 3.3 3.8 + - - +
2175A LEU* 1.3 75.5 - - - +
2177A PHE* 1.3 66.5 + - + +
2179A TYR* 3.1 26.0 - - - +
2180A VAL* 3.1 8.0 + - + +
2203A PHE* 3.9 23.6 - - + -
2206A VAL* 4.7 9.0 - - + +
2207A VAL* 4.1 24.7 - - + +
2210A CYS* 3.8 17.0 - - + -
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Residues in contact with PHE2177 (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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2128A ILE* 3.8 31.2 - - + -
2156A PHE* 3.9 22.2 - + + -
2157A GLN* 3.5 18.6 - - - -
2158A SER* 3.5 37.5 - - - -
2173A HIS* 3.2 25.3 + - + +
2174A LYS* 4.4 1.3 - - - +
2176A ILE* 1.3 84.8 - - + +
2178A GLN* 1.3 59.4 + - - +
2179A TYR 3.2 0.2 - - - -
2180A VAL* 3.1 19.6 + - + +
2181A GLU* 2.8 38.0 + - + +
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Residues in contact with GLN2178 (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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2174A LYS* 3.1 44.6 + - + +
2175A LEU* 3.5 18.2 - - - +
2176A ILE 3.3 0.2 - - - -
2177A PHE* 1.3 75.7 - - - +
2179A TYR* 1.3 56.0 + - - +
2181A GLU* 3.4 17.8 + - - +
2182A GLU* 2.9 27.1 + - - +
2237A ASN* 2.3 35.4 + - - +
2259A SER* 5.0 1.4 - - - -
2260A ALA* 4.7 7.4 + - + -
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Residues in contact with TYR2179 (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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2175A LEU 3.3 2.8 + - - +
2176A ILE 3.1 14.0 + - - +
2178A GLN* 1.3 74.1 - - - +
2180A VAL* 1.4 63.8 + - - -
2182A GLU* 2.9 8.5 + - + +
2183A LYS* 2.9 47.9 + - + +
2186A TRP* 3.3 35.7 - + - -
2202A GLU* 4.0 20.5 + - - +
2203A PHE* 4.5 5.8 - + - -
2206A VAL* 3.8 39.1 - - + +
2260A ALA* 3.8 17.9 - - + +
2261A TYR* 3.7 37.9 - + - -
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Residues in contact with VAL2180 (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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2156A PHE* 3.6 35.9 - - + -
2176A ILE 3.1 10.6 + - - +
2177A PHE* 3.1 21.0 + - + +
2179A TYR* 1.4 73.5 - - - +
2181A GLU* 1.3 64.5 + - + +
2183A LYS 3.2 0.9 + - - -
2184A GLU 2.9 18.0 + - - -
2185A SER* 3.0 33.0 + - - +
2186A TRP* 4.2 10.8 - - + -
2203A PHE* 3.7 31.4 - - + -
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Residues in contact with GLU2181 (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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2177A PHE* 2.8 21.9 + - + +
2178A GLN* 3.4 20.7 - - - +
2180A VAL* 1.3 76.1 - - + +
2182A GLU* 1.3 65.9 + - - +
2184A GLU* 2.9 21.8 + - - +
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Residues in contact with GLU2182 (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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2178A GLN 2.9 17.1 + - - +
2179A TYR* 2.9 10.7 + - + +
2181A GLU* 1.3 75.4 - - - +
2183A LYS* 1.3 73.1 + - + +
2184A GLU* 3.3 8.3 + - - +
2261A TYR* 2.8 34.5 + - - +
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Residues in contact with LYS2183 (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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2179A TYR* 2.9 42.3 + - + +
2180A VAL 4.0 2.7 - - - +
2182A GLU* 1.3 88.0 - - + +
2184A GLU* 1.3 57.9 + - - +
2185A SER 3.2 0.2 - - - -
2186A TRP* 2.7 80.3 + - + +
2187A LYS 4.2 0.5 + - - -
2202A GLU* 4.2 7.4 + - - -
2261A TYR* 5.4 1.3 + - - +
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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
------------------------------------------------------------
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