Contacts of the helix formed by residues 243 - 259 (chain A) in PDB entry 2VE7
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 PHE 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A CYS* 3.4 51.1 - - + -
235A SER* 4.3 2.0 - - - -
236A PHE* 3.9 20.4 - + + -
240A ALA* 4.6 2.2 - - + -
241A ASP* 3.7 31.9 - - - -
242A SER* 1.3 78.9 + - - +
244A ASP* 1.3 62.3 + - - +
245A GLU 3.4 2.0 - - - -
246A MET* 3.7 14.4 - - - -
247A ASN* 2.8 38.1 + - - +
130C PHE* 4.0 18.6 - + - -
2194C IPH 3.9 34.8 - + + -
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Residues in contact with ASP 244 (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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242A SER* 3.2 25.5 + - - -
243A PHE* 1.3 77.1 + - - +
245A GLU* 1.3 69.2 + - - +
246A MET 3.1 0.9 - - - -
247A ASN* 4.2 13.5 + - - +
248A ALA* 2.9 25.5 + - - +
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Residues in contact with GLU 245 (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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244A ASP* 1.3 79.9 - - - +
246A MET* 1.3 79.4 + - + +
248A ALA* 3.5 5.2 - - - +
249A GLU* 3.0 30.1 + - - +
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Residues in contact with MET 246 (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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228A TYR* 4.0 9.3 - - + -
231A LYS* 3.8 19.5 - - + +
232A CYS* 3.6 37.7 - - - +
235A SER* 3.4 35.4 - - - +
242A SER 4.8 0.2 - - - +
243A PHE* 3.6 24.7 - - - +
244A ASP 3.1 0.4 - - - -
245A GLU* 1.3 107.8 - - + +
247A ASN* 1.3 52.2 + - - +
249A GLU* 3.3 10.6 + - - +
250A LEU* 2.8 35.7 + - - +
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Residues in contact with ASN 247 (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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228A TYR* 2.7 30.9 + - - -
243A PHE* 2.8 29.4 + - - +
244A ASP* 3.4 14.6 + - - +
246A MET* 1.3 75.5 - - - +
248A ALA* 1.3 53.0 + - - +
250A LEU* 3.4 6.8 + - - +
251A GLN* 2.8 42.0 + - - +
137C THR* 5.0 0.8 + - - -
141C PHE* 4.1 24.1 - - + -
2194C IPH 4.2 16.0 - - - -
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Residues in contact with ALA 248 (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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244A ASP 2.9 18.7 + - - +
245A GLU* 3.5 5.8 - - - +
247A ASN* 1.3 73.6 - - - +
249A GLU* 1.3 60.3 + - - +
251A GLN* 3.0 14.4 + - - +
252A SER* 2.8 33.2 + - - +
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Residues in contact with GLU 249 (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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227A ASP* 5.0 0.2 - - - -
231A LYS* 3.1 41.6 + - - +
245A GLU 3.0 16.9 + - - +
246A MET* 3.7 9.0 - - - +
248A ALA* 1.3 75.0 - - - +
250A LEU* 1.3 63.2 + - - +
252A SER* 3.2 9.3 + - - -
253A LYS* 3.0 52.6 + - + +
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Residues in contact with LEU 250 (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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224A LEU* 4.1 27.8 - - + -
228A TYR* 3.7 44.0 - - + -
246A MET 2.8 21.6 + - - +
247A ASN 3.6 3.8 - - - +
249A GLU* 1.3 72.9 - - - +
251A GLN* 1.3 57.9 + - - +
253A LYS* 3.2 7.0 + - - +
254A LEU* 2.9 39.0 + - + +
138C TYR* 4.0 28.5 - - + -
141C PHE* 3.8 28.5 - - + -
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Residues in contact with GLN 251 (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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247A ASN* 2.8 31.3 + - - +
248A ALA* 3.3 10.1 + - - +
250A LEU* 1.3 72.2 - - - +
252A SER* 1.3 57.1 + - - +
254A LEU* 3.3 1.9 + - - +
255A LYS* 2.9 43.4 + - - +
141C PHE* 3.3 42.7 - - + -
144C GLN* 5.3 1.4 + - - -
145C TYR* 3.4 29.7 + - + +
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Residues in contact with SER 252 (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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248A ALA* 2.8 20.7 + - - +
249A GLU* 3.4 12.8 - - - -
251A GLN* 1.3 72.7 - - - +
253A LYS* 1.3 62.6 + - - +
255A LYS* 3.2 13.5 + - - +
256A ASP* 3.2 32.3 + - - +
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Residues in contact with LYS 253 (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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224A LEU* 3.6 29.2 - - + +
227A ASP* 2.9 30.1 + - - +
231A LYS* 3.8 2.4 - - - +
249A GLU* 3.0 46.8 + - + +
250A LEU* 3.7 7.2 - - - +
252A SER* 1.3 77.0 - - - +
254A LEU* 1.3 59.3 + - - +
256A ASP* 3.5 9.7 + - - +
257A LEU* 3.1 29.4 + - - +
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Residues in contact with LEU 254 (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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224A LEU* 3.8 24.7 - - + -
250A LEU* 2.9 30.9 + - + +
251A GLN 3.7 4.7 - - - +
253A LYS* 1.3 74.3 - - - +
255A LYS* 1.3 64.1 + - - +
257A LEU* 4.4 5.6 - - + -
258A PHE* 3.1 38.9 + - + +
138C TYR* 5.2 3.1 - - + +
141C PHE* 3.5 43.7 - - + +
142C LEU* 3.9 24.2 - - + +
145C TYR* 3.6 23.5 - - + -
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Residues in contact with LYS 255 (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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251A GLN* 2.9 26.6 + - - +
252A SER* 3.2 13.4 + - - +
254A LEU* 1.3 77.8 - - - +
256A ASP* 1.3 56.7 + - - +
259A ASN* 2.7 36.6 + - - -
260A VAL 3.5 18.5 + - - +
261A ASP* 3.8 20.7 - - - +
262A ALA 5.8 1.1 - - - +
145C TYR* 3.2 36.0 + - + -
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Residues in contact with ASP 256 (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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252A SER* 3.2 21.8 + - - +
253A LYS* 3.9 9.7 - - - +
254A LEU 3.3 0.2 - - - -
255A LYS* 1.3 79.4 - - - +
257A LEU* 1.3 63.7 + - - +
258A PHE 3.4 0.7 + - - -
259A ASN* 3.6 18.9 + - - +
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Residues in contact with LEU 257 (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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221A HIS* 3.9 42.6 - - + +
224A LEU* 4.3 19.1 - - + -
253A LYS 3.1 17.5 + - - +
254A LEU* 4.0 11.7 - - + +
255A LYS 3.4 0.2 - - - -
256A ASP* 1.3 76.6 - - - +
258A PHE* 1.3 71.6 + - + +
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Residues in contact with PHE 258 (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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220A MET* 5.5 0.4 - - + -
221A HIS* 4.3 17.7 - + - -
254A LEU* 3.1 33.4 + - + +
257A LEU* 1.3 90.1 - - + +
259A ASN* 1.3 70.0 + - - +
260A VAL* 3.2 25.1 - - + +
142C LEU* 3.7 29.2 - - + -
145C TYR* 3.7 22.7 - - + +
146C LYS* 3.7 34.8 - - + -
149C ALA* 4.2 16.8 - - + +
152C MET* 4.9 4.0 - - - +
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Residues in contact with ASN 259 (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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255A LYS 2.7 20.1 + - - -
256A ASP* 3.6 15.2 + - - +
257A LEU 5.6 0.2 - - - -
258A PHE* 1.3 74.3 - - - +
260A VAL* 1.3 57.9 + - - +
261A ASP* 4.7 2.5 - - - -
264A LYS* 3.1 49.3 + - - +
152C MET* 4.2 7.8 - - + +
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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