Contacts of the helix formed by residues 259 - 277 (chain E) in PDB entry 6C3P
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 ALA 259 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257E MET 2.9 8.9 + - - +
258E ARG* 1.3 78.9 - - - +
260E LEU* 1.3 61.9 + - - +
261E THR 3.1 0.9 - - - -
262E ASN* 3.3 4.7 + - - +
263E TYR* 2.9 28.1 + - - +
1227E LEU* 5.1 13.7 - - + -
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Residues in contact with LEU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E ILE 5.0 2.5 - - - +
256E ALA* 4.2 28.0 + - + +
258E ARG 4.6 0.4 - - - +
259E ALA* 1.3 77.4 - - - +
261E THR* 1.3 58.8 + - - +
263E TYR* 3.8 7.5 - - - +
264E GLN* 2.8 30.7 + - - +
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Residues in contact with THR 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E ALA 4.2 6.9 + - - -
258E ARG* 3.7 24.2 - - - -
259E ALA 3.1 1.2 - - - +
260E LEU* 1.3 79.0 - - - +
262E ASN* 1.3 56.9 + - - +
264E GLN* 3.3 6.0 + - - +
265E ARG* 2.9 29.3 + - - +
386E ASN* 4.9 18.6 - - - -
390E ALA* 4.7 14.3 - - - +
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Residues in contact with ASN 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ARG 3.6 17.3 + - - +
259E ALA* 3.3 8.0 + - - +
261E THR* 1.3 78.2 - - - +
263E TYR* 1.3 58.4 + - - +
265E ARG* 3.3 7.8 + - - +
266E LEU* 2.9 28.8 + - - +
390E ALA* 4.9 6.7 - - - +
393E THR* 4.0 26.7 - - + -
1227E LEU* 6.6 0.2 - - + -
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Residues in contact with TYR 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E ALA 2.9 17.1 + - - +
260E LEU* 3.8 7.9 - - - +
262E ASN* 1.3 76.0 - - - +
264E GLN* 1.3 55.9 + - - +
266E LEU* 3.3 6.9 + - - +
267E CYS* 2.9 30.9 + - - +
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Residues in contact with GLN 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E LEU 2.8 21.7 + - - +
261E THR* 3.6 7.0 - - - +
263E TYR* 1.3 71.3 - - - +
265E ARG* 1.3 58.5 + - - +
267E CYS* 3.3 6.2 + - - +
268E GLU* 2.8 31.5 + - - +
294E ALA* 4.8 6.2 - - + +
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Residues in contact with ARG 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E THR 2.9 18.2 + - - +
262E ASN* 3.6 7.2 - - - +
264E GLN* 1.3 75.4 - - - +
266E LEU* 1.3 58.7 + - - +
268E GLU* 3.4 5.1 + - - +
269E ALA* 2.9 30.5 + - - +
294E ALA* 4.8 7.9 - - + -
390E ALA* 4.7 13.9 - - + -
394E LYS* 4.9 20.0 + - - +
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Residues in contact with LEU 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ASN 2.9 17.1 + - - +
263E TYR* 3.7 7.2 - - - +
265E ARG* 1.3 75.8 - - - +
267E CYS* 1.3 58.2 + - - +
269E ALA* 3.3 7.2 + - - +
270E PHE* 2.9 27.6 + - - +
394E LYS* 6.1 2.2 - - - +
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Residues in contact with CYS 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E TYR 2.9 17.4 + - - +
264E GLN* 3.8 6.5 - - - +
266E LEU* 1.3 76.5 - - - +
268E GLU* 1.3 59.0 + - - +
270E PHE* 3.2 8.7 + - - +
271E ASP* 2.9 26.5 + - - +
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Residues in contact with GLU 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E GLN 2.8 18.1 + - - +
265E ARG 3.9 1.6 - - - +
267E CYS* 1.3 74.8 - - - +
269E ALA* 1.3 62.2 + - - +
271E ASP* 3.3 8.3 + - - +
272E ALA* 2.9 28.8 + - - +
290E ALA* 4.5 5.0 - - - +
293E HIS* 4.1 8.6 + - + +
294E ALA* 3.4 37.9 - - + +
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Residues in contact with ALA 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E ARG 2.9 17.6 + - - +
266E LEU* 3.6 7.4 - - - +
268E GLU* 1.3 75.7 - - - +
270E PHE* 1.3 58.1 + - - +
272E ALA* 3.4 7.1 + - - +
273E GLN* 2.9 29.3 + - - +
290E ALA* 4.5 13.4 - - + +
394E LYS* 5.0 12.1 - - - +
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Residues in contact with PHE 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E LEU 2.9 13.4 + - - +
267E CYS* 3.3 12.6 - - - +
269E ALA* 1.3 76.8 - - - +
271E ASP* 1.3 56.1 + - - +
273E GLN* 3.2 7.0 + - - +
274E VAL* 2.9 29.5 + - - +
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Residues in contact with ASP 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E CYS 2.9 13.1 + - - +
268E GLU* 3.3 10.5 + - - +
270E PHE* 1.3 76.0 - - - +
272E ALA* 1.3 57.8 + - - +
274E VAL* 3.3 8.0 + - - +
275E ARG* 2.9 26.5 + - - +
293E HIS* 3.7 23.0 - - + -
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Residues in contact with ALA 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E GLU 2.9 17.2 + - - +
269E ALA 3.8 4.5 - - - +
271E ASP* 1.3 76.9 - - - +
273E GLN* 1.3 58.0 + - - +
275E ARG* 3.4 9.1 - - - +
276E LYS* 2.9 24.9 + - - +
289E GLN* 5.4 3.4 - - + -
290E ALA* 4.3 26.0 - - + +
293E HIS* 4.3 10.7 + - + +
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Residues in contact with GLN 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E ALA 2.9 17.9 + - - +
270E PHE* 3.2 7.6 + - - +
272E ALA* 1.3 75.4 - - - +
274E VAL* 1.3 53.7 + - - +
276E LYS* 2.9 9.2 + - + +
277E ASP* 2.4 39.4 + - - +
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Residues in contact with VAL 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E PHE 2.9 13.3 + - - +
271E ASP* 3.3 10.5 + - - +
273E GLN* 1.3 77.0 - - - +
275E ARG* 1.3 60.8 + - - +
277E ASP* 3.2 25.8 + - - +
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Residues in contact with ARG 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E ASP 2.9 13.7 + - - +
272E ALA* 3.4 13.9 - - - +
274E VAL* 1.3 78.2 - - - +
276E LYS* 1.3 60.8 + - - +
277E ASP 4.2 3.3 - - - +
293E HIS* 6.4 0.9 - - + -
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Residues in contact with LYS 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E ALA 2.9 16.0 + - - +
273E GLN* 2.9 11.6 + - - +
275E ARG* 1.3 75.7 - - - +
277E ASP* 1.3 65.2 + - - +
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Residues in contact with ASP 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E GLN 2.4 30.0 + - - +
274E VAL* 3.2 21.3 + - - +
275E ARG 4.2 2.7 - - - +
276E LYS* 1.3 74.2 - - - +
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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