Contacts of the helix formed by residues 2090 - 2102 (chain B) in PDB entry 2H7C
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 ASP2090 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B COA 2.4 88.8 + - - +
2089B GLN* 1.3 74.0 - - - +
2091B PRO* 1.3 65.8 - - - +
2092B LYS 2.9 14.2 + - - -
2093B ALA* 3.2 7.0 + - + -
2094B GLY* 2.9 28.1 + - - -
2146B VAL* 4.5 2.2 - - + +
2295B LEU* 4.2 8.0 - - - +
2298B THR* 5.2 7.7 - - + +
2299B LEU* 4.7 5.3 - - + +
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Residues in contact with PRO2091 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B COA 5.2 0.9 - - - +
2086B MET* 4.6 5.7 - - + +
2089B GLN 3.2 4.9 - - - +
2090B ASP* 1.3 89.7 - - - +
2092B LYS* 1.3 61.7 - - + +
2094B GLY* 4.0 0.3 - - - -
2095B GLN* 3.1 29.8 + - - +
2112B LEU* 3.4 33.9 - - + -
2295B LEU* 4.6 13.2 - - + -
2299B LEU* 5.3 5.2 - - + -
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Residues in contact with LYS2092 (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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2B COA 3.8 15.5 - - + +
2090B ASP* 2.9 6.1 + - - +
2091B PRO* 1.3 78.2 - - + +
2093B ALA* 1.3 66.8 + - - +
2095B GLN* 3.4 4.0 + - - +
2096B LEU* 3.0 25.6 + - - +
4300D LYS 3.7 14.5 + - - -
4301D MET* 3.4 8.9 + - - +
4302D LYS* 2.9 65.1 - - + +
4307D ASP* 5.2 0.4 + - - -
4309D GLN* 5.6 5.1 - - + +
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Residues in contact with ALA2093 (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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2B COA 2.9 79.9 + - + +
2090B ASP* 3.2 10.5 + - + -
2092B LYS* 1.3 78.1 - - - +
2094B GLY* 1.3 63.1 + - - +
2096B LEU* 3.3 4.0 + - - +
2097B LEU 3.0 19.2 + - - -
2146B VAL* 4.4 2.2 - - + -
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Residues in contact with GLY2094 (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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2B COA 4.8 0.4 - - - -
2086B MET* 4.4 9.1 - - - +
2089B GLN* 3.2 28.0 - - - +
2090B ASP 2.9 13.8 + - - -
2091B PRO 4.0 0.7 - - - -
2093B ALA* 1.3 78.3 - - - +
2095B GLN* 1.3 60.3 + - - +
2097B LEU* 3.6 2.3 + - - +
2098B SER* 3.1 23.4 + - - -
2146B VAL* 4.2 7.3 - - - +
2147B GLY* 5.0 3.6 + - - -
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Residues in contact with GLN2095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2086B MET* 4.6 5.0 - - + +
2091B PRO 3.1 18.4 + - - +
2092B LYS* 4.0 4.2 - - - +
2094B GLY* 1.3 73.4 - - - +
2096B LEU* 1.3 66.7 + - - +
2098B SER* 3.4 6.2 + - - -
2099B GLU* 3.0 23.1 + - + +
2107B ASN* 4.1 13.5 + - - +
2109B PRO* 3.8 32.1 - - - +
2110B LEU 5.1 0.8 - - - +
4309D GLN* 3.5 37.3 + - + +
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Residues in contact with LEU2096 (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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2B COA 3.7 39.9 - - + +
2092B LYS 3.0 18.3 + - - +
2093B ALA* 3.6 5.4 - - - +
2094B GLY 3.3 0.2 - - - -
2095B GLN* 1.3 78.0 - - - +
2097B LEU* 1.3 63.6 + - - +
2099B GLU* 3.2 7.9 + - + +
2100B LEU* 3.0 45.8 + - + +
2361B MET* 4.3 6.1 - - + -
2363B LEU* 3.8 17.0 - - + -
2459B MET* 5.3 4.0 - - + -
4308D LEU* 4.5 26.5 - - + +
4309D GLN* 4.9 12.5 - - + +
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Residues in contact with LEU2097 (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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2B COA 3.0 57.6 + - - +
2093B ALA 3.0 9.4 + - - +
2094B GLY 4.0 3.4 - - - +
2096B LEU* 1.3 77.1 - - - +
2098B SER* 1.3 64.8 + - - +
2100B LEU* 3.1 9.8 + - + +
2101B PHE* 2.9 59.2 + - + +
2141B GLY 4.1 8.1 - - - +
2142B GLY* 3.8 12.1 - - - +
2146B VAL* 3.8 13.2 - - + -
2147B GLY* 4.5 9.0 - - - +
2152B TYR* 5.6 1.3 - - - +
2358B LEU* 5.0 0.4 - - + -
2363B LEU* 4.3 6.7 - - + -
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Residues in contact with SER2098 (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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2086B MET* 6.2 2.2 - - - -
2094B GLY 3.1 18.8 + - - -
2095B GLN* 3.5 7.4 - - - -
2097B LEU* 1.3 77.5 - - - +
2099B GLU* 1.3 57.0 + - - +
2102B THR* 2.8 36.4 + - - -
2107B ASN* 2.8 25.9 + - - -
2108B ILE 4.9 3.3 + - - -
2110B LEU* 5.1 6.5 - - - +
2148B ALA* 6.1 0.9 - - - -
2151B THR* 2.7 32.4 + - - +
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Residues in contact with GLU2099 (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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2095B GLN* 3.0 19.0 + - + +
2096B LEU* 3.7 9.2 - - + +
2098B SER* 1.3 77.2 - - - +
2100B LEU* 1.3 62.3 + - + +
2102B THR* 3.8 11.7 - - - +
2107B ASN* 3.8 23.3 + - + +
2482B LYS* 5.6 1.2 + - - -
4309D GLN* 5.8 4.9 - - + +
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Residues in contact with LEU2100 (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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2096B LEU* 3.0 36.6 + - + +
2097B LEU* 3.6 7.6 - - + +
2099B GLU* 1.3 79.5 - - + +
2101B PHE* 1.3 69.6 + - + +
2357B TRP* 4.5 9.2 - - + -
2358B LEU* 3.6 18.4 - - + -
2361B MET* 3.6 28.5 - - + -
2363B LEU* 4.3 4.7 - - + -
2455B PHE 5.1 1.7 - - - +
2457B SER* 3.6 33.2 - - - +
2459B MET* 5.5 3.4 - - + -
2473B PHE* 3.3 21.9 - - - -
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Residues in contact with PHE2101 (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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2B COA 5.2 4.5 - - - -
2097B LEU* 2.9 38.7 + - + +
2100B LEU* 1.3 88.5 - - + +
2102B THR* 1.3 67.0 + - - +
2103B ASN* 3.5 2.6 + - - +
2141B GLY 5.9 4.0 - - - -
2142B GLY 6.0 0.4 - - - -
2151B THR* 4.0 5.8 - - + -
2152B TYR* 3.6 36.6 - - + +
2220B GLU* 3.9 20.0 - - - -
2358B LEU* 3.2 41.1 - - + -
2468B HIS* 4.1 3.1 - + - -
2469B GLY* 4.0 25.8 - - - -
2472B LEU* 3.6 22.5 - - + +
2473B PHE* 4.2 11.7 - + - -
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Residues in contact with THR2102 (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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2098B SER 2.8 23.9 + - - +
2099B GLU 3.8 12.0 - - - +
2101B PHE* 1.3 76.0 - - - +
2103B ASN* 1.3 55.7 + - - +
2104B ARG* 2.8 43.4 - - + +
2107B ASN* 3.8 26.4 + - + +
2151B THR* 2.8 24.9 + - - +
2473B PHE* 3.4 8.7 - - - -
2482B LYS* 3.2 18.8 - - - +
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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