Contacts of the helix formed by residues 279 - 299 (chain E) in PDB entry 3CQ6
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 GLY 279 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E ALA 3.5 9.4 + - - -
276E ASP 3.2 9.8 + - - -
277E THR 3.2 2.2 - - - -
278E LEU* 1.3 73.6 - - - +
280E THR* 1.3 63.9 + - - +
281E VAL 3.0 2.9 + - - -
282E GLU* 3.4 28.7 + - - +
283E LYS* 4.0 7.4 + - - +
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Residues in contact with THR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASN* 2.9 24.0 + - - +
39E TYR* 3.5 42.6 - - + -
229E ALA 4.4 2.1 + - - -
231E ASP* 5.8 2.2 - - - +
276E ASP 4.2 3.3 + - - +
277E THR* 2.9 19.1 + - + +
278E LEU 4.4 0.7 - - - -
279E GLY* 1.3 76.9 - - - +
281E VAL* 1.3 59.2 + - - +
283E LYS* 3.2 14.6 + - + +
284E LEU* 2.9 31.8 + - - +
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Residues in contact with VAL 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E GLU* 3.6 24.7 - - + +
203E PHE* 3.9 17.9 - - + -
229E ALA* 3.9 28.0 - - + -
278E LEU* 3.2 28.0 - - + +
279E GLY 3.0 0.6 - - - -
280E THR* 1.3 81.1 - - - +
282E GLU* 1.3 56.8 + - + +
284E LEU* 4.0 6.6 - - + +
285E SER* 2.7 47.4 + - - +
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Residues in contact with GLU 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E LEU 5.4 0.2 - - - +
279E GLY* 3.4 19.0 + - - +
280E THR 3.2 0.2 - - - -
281E VAL* 1.3 79.4 - - + +
283E LYS* 1.3 63.4 + - + +
285E SER* 3.9 4.2 - - - -
286E VAL* 3.4 28.1 + - - +
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Residues in contact with LYS 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E TYR* 3.7 37.7 + - + +
279E GLY 4.5 5.4 - - - +
280E THR* 3.2 18.4 + - + +
282E GLU* 1.3 79.4 - - + +
284E LEU* 1.3 64.7 + - - +
285E SER 3.4 0.2 + - - -
286E VAL* 3.4 6.2 + - - +
287E GLU* 3.2 28.6 + - + +
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Residues in contact with LEU 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASN* 3.7 34.3 - - + +
38E PRO* 3.7 15.3 - - + -
39E TYR* 4.2 8.5 - - + -
203E PHE* 4.0 28.3 - - + -
280E THR* 2.9 23.0 + - - +
281E VAL* 4.0 3.6 - - - +
283E LYS* 1.3 77.2 - - - +
285E SER* 1.3 58.1 + - - +
287E GLU* 3.4 2.8 + - - -
288E ARG* 3.0 27.2 + - - +
307E SER 5.4 0.6 - - - +
308E ASN* 5.0 8.4 - - + +
345E ILE* 3.5 36.7 - - + +
346E GLY 3.7 16.6 - - - +
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Residues in contact with SER 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E PHE* 4.1 18.7 + - - +
281E VAL* 2.7 35.5 + - - +
282E GLU* 3.9 6.3 - - - -
283E LYS 3.2 0.4 - - - -
284E LEU* 1.3 77.7 - - - +
286E VAL* 1.3 60.3 + - - +
288E ARG* 3.6 24.5 + - - +
289E VAL* 3.5 22.9 + - - +
307E SER 5.5 1.5 + - - -
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Residues in contact with VAL 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E GLU 3.4 17.3 + - - +
283E LYS* 4.0 6.1 - - - +
284E LEU 3.3 0.4 - - - -
285E SER* 1.3 74.6 - - - +
287E GLU* 1.3 67.5 + - + +
288E ARG 3.2 0.2 - - - -
289E VAL* 3.0 10.9 + - + +
290E ARG* 2.9 27.6 + - + +
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Residues in contact with GLU 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E TYR* 6.0 0.9 - - - +
283E LYS* 3.2 18.0 + - + +
284E LEU* 3.8 1.3 - - - +
286E VAL* 1.3 78.4 - - + +
288E ARG* 1.3 67.8 + - - +
290E ARG* 2.7 51.0 + - - +
291E VAL* 2.8 27.0 + - - +
345E ILE* 3.5 20.6 - - + -
346E GLY 4.7 3.1 - - - +
348E PRO* 3.5 22.1 - - + +
351E ASN* 3.0 19.9 + - - +
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Residues in contact with ARG 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E PHE* 4.4 4.9 + - - +
284E LEU 3.0 15.0 + - - +
285E SER* 3.6 32.0 + - - +
286E VAL 3.2 0.2 - - - -
287E GLU* 1.3 76.9 - - - +
289E VAL* 1.3 75.1 + - - +
291E VAL* 3.2 1.6 + - - +
292E ALA* 2.8 32.2 + - - +
305E SER* 2.9 40.6 + - - +
306E GLU* 3.8 19.9 + - - +
307E SER 3.0 24.1 + - - +
309E PHE 4.1 2.0 - - - +
310E VAL* 3.9 18.8 - - + +
345E ILE* 3.6 20.1 - - + +
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Residues in contact with VAL 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285E SER 3.5 13.2 + - - +
286E VAL* 3.0 14.0 + - + +
288E ARG* 1.3 97.5 - - - +
290E ARG* 1.3 59.2 + - - +
292E ALA* 3.6 5.9 + - - +
293E ALA* 3.0 32.9 + - + +
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Residues in contact with ARG 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E VAL* 2.9 16.1 + - + +
287E GLU* 2.7 48.3 + - - +
289E VAL* 1.3 79.3 - - - +
291E VAL* 1.3 62.2 + - - +
293E ALA* 3.3 6.4 + - - +
294E ARG* 3.0 25.7 + - + +
348E PRO* 3.6 16.2 + - - +
351E ASN* 3.9 6.8 - - - +
352E ASP* 3.2 27.4 + - - -
355E LEU* 3.8 18.4 - - + +
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Residues in contact with VAL 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E GLU* 2.8 24.1 + - - +
288E ARG 3.7 2.9 - - - +
290E ARG* 1.3 76.0 - - + +
292E ALA* 1.3 57.4 + - - +
294E ARG* 3.3 2.3 + - - +
295E LEU* 3.0 35.2 + - + +
310E VAL* 4.6 2.5 - - + -
343E THR* 4.6 5.2 - - + -
345E ILE* 3.7 22.9 - - + -
351E ASN* 3.7 31.6 - - + +
354E PHE* 3.7 28.3 - - + -
355E LEU* 4.0 19.0 - - + +
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Residues in contact with ALA 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E ARG* 2.8 23.8 + - + +
289E VAL* 3.9 5.4 - - - +
291E VAL* 1.3 75.4 - - - +
293E ALA* 1.3 61.2 + - - +
295E LEU* 3.7 4.6 + - - -
296E GLU* 3.2 31.0 + - - +
302E VAL* 3.9 24.3 - - + +
303E VAL 5.8 0.4 - - - +
304E PRO* 6.4 0.7 - - + -
305E SER* 6.3 0.9 - - - +
310E VAL* 4.2 13.2 - - + -
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Residues in contact with ALA 293 (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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289E VAL* 3.0 23.3 + - + +
290E ARG* 3.6 6.5 - - - +
291E VAL 3.2 0.2 - - - -
292E ALA* 1.3 76.3 - - - +
294E ARG* 1.3 58.3 + - - +
296E GLU* 3.2 13.0 + - - +
297E GLU* 2.9 27.9 + - - +
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Residues in contact with ARG 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E ARG* 3.0 18.3 + - + +
291E VAL 3.8 3.6 - - - +
293E ALA* 1.3 74.4 - - - +
295E LEU* 1.3 57.9 + - - +
297E GLU* 3.2 36.7 + - - +
298E LEU* 2.9 59.3 + - + +
355E LEU* 3.6 32.6 + - + +
359E ALA* 5.0 7.3 - - - +
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Residues in contact with LEU 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E VAL* 3.0 24.7 + - + +
292E ALA* 3.9 0.7 - - - +
294E ARG* 1.3 75.0 - - - +
296E GLU* 1.3 61.1 + - - +
298E LEU* 3.2 5.9 + - + +
299E GLY 3.1 5.4 + - - -
300E TYR* 3.0 43.3 + - + +
302E VAL* 3.7 13.0 - - + -
310E VAL* 4.0 21.3 - - + -
312E PHE* 4.0 26.5 - - + -
354E PHE* 3.7 34.1 - - + -
355E LEU* 4.1 5.6 - - + -
358E ALA* 3.7 22.7 - - + -
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Residues in contact with GLU 296 (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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292E ALA* 3.2 16.0 + - - +
293E ALA* 3.5 13.3 - - - +
295E LEU* 1.3 79.8 - - - +
297E GLU* 1.3 59.4 + - - +
299E GLY* 3.2 14.4 + - - -
300E TYR 3.9 11.5 - - - +
302E VAL* 3.6 32.6 + - + +
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Residues in contact with GLU 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E ALA 2.9 14.2 + - - +
294E ARG* 3.2 42.8 + - - +
296E GLU* 1.3 76.4 - - - +
298E LEU* 1.3 61.8 + - - +
299E GLY* 3.5 0.7 + - - -
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Residues in contact with LEU 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E ARG* 2.9 66.6 + - + +
295E LEU* 3.2 11.2 + - + +
297E GLU* 1.3 78.5 - - - +
299E GLY* 1.3 57.4 + - - +
300E TYR* 4.0 11.2 - - + -
355E LEU* 4.1 9.4 - - - +
358E ALA* 4.3 10.1 - - + -
359E ALA* 3.9 37.2 - - + +
362E ILE* 3.3 20.2 - - + +
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Residues in contact with GLY 299 (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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295E LEU 3.1 1.8 + - - -
296E GLU 3.2 10.7 + - - -
297E GLU 3.2 1.3 - - - -
298E LEU* 1.3 79.5 - - - +
300E TYR* 1.3 65.6 + - - +
301E ALA 3.9 0.3 + - - -
362E ILE* 3.7 10.9 - - - +
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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
------------------------------------------------------------
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