Contacts of the helix formed by residues 265 - 280 (chain A) in PDB entry 4D1Q
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 CYS 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A VAL* 4.6 2.0 - - - -
247A THR 2.9 19.8 + - - +
248A ASP* 4.0 7.9 - - - +
249A ARG* 6.1 0.2 - - - +
263A ILE 3.7 0.2 + - - -
264A ASN* 1.3 69.7 - - - +
266A SER* 1.3 57.3 + - - +
267A SER* 3.2 11.9 - - - -
268A HIS* 3.2 31.7 - - + +
269A LEU* 3.0 25.8 + - - +
566A ALA 4.2 0.2 - - - -
567A SER* 3.0 37.0 - - - +
568A SER* 3.4 21.3 - - - +
569A ALA 4.9 0.9 - - - -
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASN 3.0 10.1 + - - -
265A CYS* 1.3 69.9 - - - +
267A SER* 1.3 61.0 + - - +
269A LEU* 3.6 8.1 - - - +
270A LEU* 2.9 28.6 + - - +
374A LEU* 3.6 25.0 - - - +
385A VAL* 3.6 13.6 - - - +
421A TRP* 3.5 22.6 + - - -
425A LEU* 4.7 1.0 - - - +
429A HIS* 3.8 10.6 + - - -
566A ALA 3.2 16.7 + - - -
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Residues in contact with SER 267 (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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265A CYS* 3.1 10.1 - - - -
266A SER* 1.3 76.1 - - - +
268A HIS* 1.3 70.4 + - - +
270A LEU* 3.1 2.1 + - - -
271A SER* 3.0 18.2 + - - -
319A TRP* 3.4 36.8 - - - -
371A PHE* 3.4 24.3 + - - -
374A LEU* 4.2 9.0 - - - +
375A GLN* 3.9 10.2 - - - +
567A SER* 3.7 16.0 + - - -
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Residues in contact with HIS 268 (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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180A ASP* 4.2 1.8 + - - -
248A ASP* 3.1 33.7 - - + +
249A ARG 5.1 1.6 - - - +
265A CYS* 3.2 19.5 - - + +
267A SER* 1.3 80.4 - - - +
269A LEU* 1.3 65.9 + - + +
270A LEU 3.0 0.2 + - - -
271A SER* 3.1 7.1 + - - -
272A ASN* 3.1 29.5 + - - +
319A TRP* 3.2 30.2 - + - +
568A SER* 3.5 10.7 + - - -
572A GLU* 3.3 25.6 + - - -
16D G 3.6 20.1 + - + +
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Residues in contact with LEU 269 (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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249A ARG* 3.6 39.9 - - + +
264A ASN* 4.4 10.3 - - + +
265A CYS 3.0 22.4 + - - +
266A SER* 3.6 9.9 - - - +
267A SER 3.2 0.2 - - - -
268A HIS* 1.3 76.7 - - + +
270A LEU* 1.3 64.1 + - - +
272A ASN* 3.1 9.6 + - - +
273A VAL* 3.1 18.6 + - - +
420A ILE* 3.3 27.8 - - + +
421A TRP* 3.2 38.4 - - + +
424A ASN* 3.7 16.6 - - + +
425A LEU* 5.0 1.1 - - + -
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Residues in contact with LEU 270 (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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266A SER 2.9 21.4 + - - +
267A SER* 3.5 4.0 - - - +
268A HIS 3.0 0.2 + - - -
269A LEU* 1.3 69.1 - - - +
271A SER* 1.3 55.2 + - - +
273A VAL* 2.6 36.4 + - + +
274A LEU* 2.8 10.2 + - + -
367A PHE* 3.7 32.5 - - + +
370A ILE* 3.7 29.6 - - + -
371A PHE* 3.4 39.3 - - + -
374A LEU* 5.5 1.6 - - + -
392A VAL* 4.7 3.1 - - + -
421A TRP* 3.9 29.3 - - + -
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Residues in contact with SER 271 (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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267A SER 3.0 11.0 + - - -
268A HIS* 3.5 9.2 - - - -
270A LEU* 1.3 75.9 - - - +
272A ASN* 1.3 59.1 + - - +
274A LEU* 3.1 7.5 + - - +
275A GLU* 2.8 35.8 + - - +
318A ARG 5.0 2.3 + - - -
319A TRP* 3.7 31.5 - - - -
320A ASN 5.3 1.3 + - - -
371A PHE* 3.5 12.1 - - - -
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Residues in contact with ASN 272 (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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249A ARG* 3.0 30.7 - - - +
268A HIS* 3.1 21.5 + - - +
269A LEU* 3.4 16.4 - - - +
270A LEU 2.9 0.4 + - - -
271A SER* 1.3 74.3 - - - +
273A VAL* 1.3 68.3 + - - +
275A GLU* 4.1 15.7 - - + +
276A ASN* 3.0 30.7 + - - +
420A ILE* 4.0 14.4 - - + -
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Residues in contact with VAL 273 (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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269A LEU 3.1 9.2 + - - +
270A LEU* 2.6 29.6 + - + +
272A ASN* 1.3 71.5 - - - +
274A LEU* 1.3 58.3 + - + +
277A SER* 2.8 38.3 + - - +
367A PHE* 4.8 8.5 - - + -
413A ILE* 4.1 20.2 - - + +
416A ASN* 3.4 32.8 - - + +
417A VAL* 3.7 15.9 - - + +
420A ILE* 3.7 22.0 - - + -
421A TRP* 4.2 9.0 - - + +
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Residues in contact with LEU 274 (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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270A LEU 2.8 10.7 + - - +
271A SER* 3.6 8.5 - - - +
273A VAL* 1.3 80.1 - - + +
275A GLU* 1.3 64.7 + - - +
277A SER* 3.7 3.5 - - - -
278A PHE* 3.2 36.2 + - + +
320A ASN* 3.1 31.9 - - - +
364A LEU* 4.1 17.7 - - + -
367A PHE* 3.4 43.3 - - + -
371A PHE* 3.7 18.6 - - + -
413A ILE* 5.0 9.6 - - + -
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Residues in contact with GLU 275 (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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271A SER* 2.8 23.8 + - - +
272A ASN* 3.6 18.6 - - + +
274A LEU* 1.3 73.9 - - - +
276A ASN* 1.3 79.7 + - - +
278A PHE* 3.2 5.4 + - - +
279A GLU* 3.1 23.1 + - - +
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Residues in contact with ASN 276 (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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272A ASN* 3.0 21.7 + - - +
275A GLU* 1.3 85.3 - - - +
277A SER* 1.3 63.9 + - - +
279A GLU* 4.4 13.1 - - - +
280A GLU* 3.0 43.8 + - - +
416A ASN* 3.7 13.1 - - - +
419A ILE* 6.1 0.6 - - - +
420A ILE* 3.8 18.0 - - + +
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Residues in contact with SER 277 (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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273A VAL 2.8 23.6 + - - -
274A LEU* 3.7 5.8 - - - -
275A GLU 3.2 0.2 - - - -
276A ASN* 1.3 75.1 - - - +
278A PHE* 1.3 67.3 + - - +
280A GLU* 3.3 7.4 + - - +
281A THR* 3.1 20.1 + - - -
409A LEU* 3.9 3.8 - - - +
412A ASN* 4.2 2.4 - - - +
413A ILE* 2.9 46.4 + - - -
416A ASN* 2.8 21.2 + - - +
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Residues in contact with PHE 278 (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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274A LEU* 3.2 26.5 + - + +
275A GLU* 3.7 7.9 - - - +
277A SER* 1.3 75.6 - - - +
279A GLU* 1.3 57.7 + - - +
281A THR* 2.6 36.8 + - - +
282A PRO* 4.8 0.2 - - - +
284A LEU* 5.0 4.7 - - + -
285A ASN* 5.3 0.9 + - - -
288A ILE* 4.7 9.9 - - + -
322A THR* 3.6 35.0 - - + -
360A MET* 3.5 34.3 - - + -
364A LEU* 4.3 24.0 - - + -
409A LEU* 3.6 28.5 - - + -
413A ILE* 5.5 0.9 - - + -
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Residues in contact with GLU 279 (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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275A GLU* 3.1 14.3 + - - +
276A ASN* 3.9 13.5 - - - +
278A PHE* 1.3 79.7 - - - +
280A GLU* 1.3 68.4 + - + +
281A THR 3.0 4.9 + - - -
282A PRO* 3.7 12.6 - - - +
285A ASN* 5.0 4.2 + - - +
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Residues in contact with GLU 280 (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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276A ASN* 3.0 39.1 + - - +
277A SER 4.1 1.1 - - - +
278A PHE 2.8 1.6 + - - -
279A GLU* 1.3 86.4 - - + +
281A THR* 1.3 64.0 + - - +
282A PRO* 3.3 8.5 - - - +
408A LYS* 4.2 8.1 - - - +
412A ASN* 3.4 20.2 + - - +
415A LYS* 2.6 37.3 + - - +
416A ASN* 3.6 11.2 + - - +
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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