Contacts of the helix formed by residues 2178 - 2192 (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 PRO2178 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2176B TYR* 3.8 13.2 - - + +
2177B MET* 1.4 85.3 - - + +
2179B ILE* 1.3 67.5 + - - +
2180B GLU* 2.9 7.9 + - + +
2181B ALA* 3.0 9.7 + - + +
2182B PHE* 2.9 19.1 + - - -
2220B GLY 3.1 25.1 - - - +
2222B ARG* 3.9 24.0 - - + -
2282B PRO* 3.8 17.0 - - + +
2283B PHE* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2177B MET 3.6 2.0 + - - -
2178B PRO* 1.3 69.2 - - - +
2180B GLU* 1.3 59.5 + - - +
2182B PHE* 3.5 9.3 - - + +
2183B LEU* 3.0 41.6 + - + +
2200B PRO* 5.3 3.4 - - + -
2278B ARG 5.8 1.6 - - - +
2279B HIS* 6.3 2.9 - - - -
2281B LEU 4.4 8.1 - - - +
2282B PRO 3.0 11.5 + - - +
2283B PHE* 3.6 33.3 - - - +
2284B GLU* 3.8 10.1 - - + +
2382B GLY* 3.2 32.1 - - - +
2384B VAL* 4.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2178B PRO* 2.9 7.5 + - + +
2179B ILE* 1.3 77.3 - - - +
2181B ALA* 1.3 64.6 + - - +
2183B LEU* 3.2 10.0 + - - +
2184B ARG* 3.1 35.3 + - + +
2282B PRO 4.3 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2177B MET* 3.9 11.1 - - + +
2178B PRO* 3.0 10.2 + - + +
2180B GLU* 1.3 78.3 - - - +
2182B PHE* 1.3 60.2 + - - +
2183B LEU 3.1 0.2 - - - -
2184B ARG* 3.0 34.6 + - - +
2185B LEU* 2.8 33.4 + - - +
2220B GLY* 3.7 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2177B MET* 3.6 14.0 - - - +
2178B PRO 2.9 12.7 + - - +
2179B ILE* 3.5 14.6 - - + +
2181B ALA* 1.3 77.9 - - - +
2183B LEU* 1.3 76.2 + - + +
2185B LEU* 3.6 2.3 + - - +
2186B ASN* 3.2 49.3 + - - +
2197B PHE* 4.1 4.7 - - + -
2198B LYS 4.1 2.9 - - - -
2199B ASN* 3.2 44.4 - - - -
2200B PRO* 3.5 31.2 - - + -
2203B ALA* 3.9 14.1 - - + -
2381B ALA* 4.7 7.4 - - + -
2382B GLY* 4.3 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2179B ILE* 3.0 31.4 + - + +
2180B GLU* 3.6 9.2 - - - +
2181B ALA 3.1 0.4 - - - -
2182B PHE* 1.3 99.4 - - + +
2184B ARG* 1.3 62.1 + - - +
2186B ASN* 4.0 7.4 - - + +
2187B GLU* 3.1 37.7 + - - +
2381B ALA 5.8 0.7 - - - +
2384B VAL* 5.1 11.0 - - + -
2385B ILE* 4.3 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2180B GLU* 3.1 29.3 + - - +
2181B ALA* 3.0 35.6 + - - +
2183B LEU* 1.3 77.3 - - - +
2185B LEU* 1.3 59.4 + - - +
2187B GLU* 3.3 11.1 + - + +
2188B GLU* 3.0 52.5 + - + +
2218B LYS 4.4 8.5 + - - -
2219B ARG* 5.3 0.4 - - - +
2220B GLY* 3.9 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2177B MET* 3.6 20.0 - - + -
2181B ALA 2.8 14.9 + - - +
2182B PHE 3.9 4.0 - - - +
2184B ARG* 1.3 75.9 - - - +
2186B ASN* 1.3 66.0 + - - +
2188B GLU* 3.2 18.0 + - - +
2189B LEU* 2.9 39.6 + - + +
2197B PHE* 3.4 26.9 - - + -
2203B ALA* 4.4 1.1 - - + -
2207B SER* 3.5 9.6 - - - +
2219B ARG* 3.2 46.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2182B PHE* 3.2 31.9 + - - +
2183B LEU* 4.4 6.9 - - + +
2184B ARG 3.4 0.2 - - - -
2185B LEU* 1.3 78.0 - - - +
2187B GLU* 1.3 52.2 + - + +
2189B LEU* 4.5 1.3 - - - -
2190B GLU* 2.5 43.2 + - - +
2196B VAL* 3.4 24.2 - - + +
2197B PHE* 2.9 54.5 + - - +
2360B HIS* 4.9 5.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2183B LEU* 3.1 33.5 + - - +
2184B ARG* 3.4 8.9 - - - +
2185B LEU 3.1 0.2 - - - -
2186B ASN* 1.3 74.5 - - - +
2188B GLU* 1.3 67.1 + - + +
2190B GLU* 3.7 11.6 - - - +
2191B GLU* 2.9 30.5 + - + +
2334B ARG* 4.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2184B ARG* 3.0 49.2 + - + +
2185B LEU* 3.2 19.4 + - - +
2187B GLU* 1.3 77.8 - - + +
2189B LEU* 1.3 65.5 + - + +
2191B GLU* 3.4 4.6 + - - +
2192B ARG* 3.3 37.9 + - - +
2218B LYS* 5.3 6.8 + - - -
2219B ARG* 5.6 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2185B LEU* 2.9 31.7 + - + +
2186B ASN* 3.7 3.8 - - - +
2188B GLU* 1.3 74.9 - - + +
2190B GLU* 1.3 61.4 + - - +
2191B GLU 2.9 6.4 + - - -
2192B ARG* 3.2 38.2 + - - +
2194B GLU* 3.2 41.9 + - + +
2195B LYS 3.6 20.4 - - - +
2196B VAL* 4.6 5.2 - - + -
2197B PHE* 3.6 33.9 - - + -
2219B ARG* 6.0 2.7 - - - +
2361B ASN* 4.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2186B ASN* 2.5 24.0 + - - +
2187B GLU* 3.8 13.1 - - - +
2189B LEU* 1.3 72.0 - - - +
2191B GLU* 1.3 57.8 + - + +
2192B ARG 3.6 0.4 + - - -
2193B GLY 4.1 2.1 + - - -
2196B VAL* 3.9 8.2 - - + +
2337B ARG* 3.0 54.2 + - - +
2339B THR* 4.1 9.0 - - - +
2358B THR* 4.4 2.9 + - - -
2360B HIS* 3.4 48.8 + - + +
2361B ASN* 3.4 17.4 + - - +
2422B VAL* 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2187B GLU* 2.9 19.5 + - + +
2188B GLU* 3.6 7.2 - - - +
2189B LEU 2.9 0.2 - - - -
2190B GLU* 1.3 77.6 - - + +
2192B ARG* 1.3 59.3 + - + +
2193B GLY 3.3 6.7 + - - -
2334B ARG* 4.9 18.1 + - - +
2335B THR* 3.2 35.7 + - - +
2337B ARG* 2.8 33.2 + - - +
2339B THR* 5.3 0.2 + - - -
2422B VAL* 4.1 13.5 - - - +
2424B ARG* 4.2 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2188B GLU* 3.3 24.6 + - - +
2189B LEU* 3.2 30.1 + - - +
2191B GLU* 1.3 79.2 - - + +
2193B GLY* 1.3 55.4 + - - +
2194B GLU* 2.8 37.7 + - + +
2421B LYS* 4.0 14.0 + - - +
2422B VAL* 4.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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