Contacts of the helix formed by residues 265 - 280 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B VAL* 5.6 1.1 - - - -
247B THR 2.9 13.0 + - - +
248B ASP* 4.1 3.8 - - - +
249B ARG* 5.6 0.4 - - - +
264B ASN* 1.3 72.0 - - - +
266B SER* 1.3 63.2 - - - +
267B SER* 3.2 13.9 - - - -
268B HIS* 3.2 34.3 - - + +
269B LEU* 2.9 24.4 + - - +
319B TRP* 4.9 1.1 - - - -
566B ALA 4.2 3.6 - - - -
567B SER* 2.9 34.8 - - - +
568B SER* 3.4 26.9 - - - +
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Residues in contact with SER 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ASN 3.1 4.2 + - - -
265B CYS* 1.3 71.3 - - - +
267B SER* 1.3 56.4 + - - +
269B LEU* 3.2 7.8 + - - +
270B LEU* 2.8 30.5 + - - +
374B LEU* 3.7 24.2 - - - -
385B VAL* 3.4 23.0 - - - +
421B TRP* 3.8 18.5 + - - +
425B LEU* 4.5 1.4 - - - +
429B HIS* 3.7 12.8 + - - -
566B ALA 3.2 18.7 + - - -
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Residues in contact with SER 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B CYS* 3.2 9.9 - - - -
266B SER* 1.3 78.1 - - - +
268B HIS* 1.3 56.0 + - - +
270B LEU* 3.3 1.6 + - - -
271B SER* 2.9 25.6 + - - -
319B TRP* 3.4 38.0 - - - -
371B PHE* 3.2 22.8 + - - -
374B LEU* 3.7 17.3 - - - +
375B GLN* 3.9 6.4 - - - +
567B SER* 3.6 15.2 + - - -
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Residues in contact with HIS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP* 4.7 1.0 + - - -
248B ASP* 3.6 34.5 - - + +
249B ARG* 5.3 2.2 - - + +
265B CYS* 3.2 27.7 - - + +
267B SER* 1.3 74.7 - - - +
269B LEU* 1.3 66.5 + - + +
271B SER* 3.2 7.9 + - - +
272B ASN* 2.9 31.4 + - - +
319B TRP* 3.5 24.3 + + - +
568B SER* 4.3 6.5 - - - -
572B GLU* 3.2 27.6 + - - -
16F G 3.8 13.3 + - + -
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 3.6 42.0 - - + +
264B ASN* 4.5 9.4 - - + +
265B CYS 2.9 16.3 + - - +
266B SER* 3.4 10.5 - - - +
268B HIS* 1.3 77.9 - - + +
270B LEU* 1.3 63.3 + - - +
272B ASN* 2.9 7.8 + - - +
273B VAL* 2.9 26.7 + - - +
420B ILE* 3.7 16.1 - - + +
421B TRP* 3.4 33.4 - - + +
424B ASN* 3.7 28.9 - - + +
425B LEU* 4.8 2.2 - - + -
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B SER 2.8 19.9 + - - +
267B SER* 3.5 5.8 - - - +
269B LEU* 1.3 71.7 - - - +
271B SER* 1.3 64.6 + - - +
273B VAL* 3.1 10.8 + - + -
274B LEU* 2.8 21.9 + - + +
367B PHE* 3.7 32.8 - - + +
370B ILE* 3.9 31.4 - - + -
371B PHE* 3.4 36.1 - - + -
374B LEU* 5.0 2.9 - - + -
392B VAL* 5.2 1.3 - - + -
421B TRP* 4.0 29.1 - - + -
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Residues in contact with SER 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER 2.9 10.2 + - - -
268B HIS* 3.2 7.8 + - - -
270B LEU* 1.3 75.9 - - - +
272B ASN* 1.3 57.3 + - - +
274B LEU* 3.7 6.7 - - - +
275B GLU* 2.9 32.8 + - - +
318B ARG 4.5 3.8 + - - -
319B TRP* 3.5 40.5 - - - -
320B ASN 4.6 2.6 + - - -
321B SER* 5.7 0.3 + - - -
371B PHE* 3.7 8.6 - - - -
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Residues in contact with ASN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 3.2 29.7 - - - +
268B HIS* 2.9 24.7 + - - +
269B LEU* 3.0 13.6 - - - +
271B SER* 1.3 76.1 - - - +
273B VAL* 1.3 62.4 + - - +
275B GLU* 3.4 19.3 + - - +
276B ASN* 3.0 35.0 + - - +
420B ILE* 3.8 14.1 - - + +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU 2.9 9.6 + - - +
270B LEU* 3.4 20.6 - - + +
272B ASN* 1.3 77.3 - - - +
274B LEU* 1.3 60.6 + - - +
276B ASN* 4.0 0.9 - - - +
277B SER* 2.9 43.2 + - - +
367B PHE* 5.1 1.6 - - + -
413B ILE* 4.3 7.0 - - + +
416B ASN* 3.7 13.8 - - + +
417B VAL* 3.9 31.2 - - + +
420B ILE* 3.5 37.2 - - + -
421B TRP* 4.1 10.3 - - + +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU 2.8 15.6 + - - +
271B SER* 3.7 7.9 - - - +
273B VAL* 1.3 78.5 - - + +
275B GLU* 1.3 61.3 + - - +
277B SER* 3.5 4.3 - - - -
278B PHE* 3.1 51.6 + - + -
320B ASN* 3.2 34.1 - - - +
322B THR* 5.7 1.1 - - - +
364B LEU* 4.3 9.6 - - + -
367B PHE* 3.7 40.4 - - + -
371B PHE* 4.0 14.6 - - + -
413B ILE* 5.0 9.0 - - + -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 2.9 18.7 + - - +
272B ASN* 3.4 22.4 - - - +
274B LEU* 1.3 75.1 - - - +
276B ASN* 1.3 80.7 + - - +
277B SER 3.1 0.5 + - - -
278B PHE* 3.3 5.3 + - - +
279B GLU* 3.1 23.2 + - - +
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Residues in contact with ASN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ASN* 3.0 21.1 + - - +
273B VAL 4.1 0.2 - - - +
275B GLU* 1.3 87.1 - - - +
277B SER* 1.3 67.8 + - - +
279B GLU* 3.2 16.8 + - - +
280B GLU* 2.9 43.3 + - - +
416B ASN* 3.9 12.2 - - - +
419B ILE* 6.2 0.4 - - - +
420B ILE* 3.7 17.9 - - + +
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 2.9 23.5 + - - +
274B LEU* 3.5 7.9 - - - -
276B ASN* 1.3 79.4 - - - +
278B PHE* 1.3 66.3 + - - +
280B GLU* 2.9 10.3 + - - +
281B THR* 3.2 15.5 + - - -
409B LEU* 4.8 3.1 - - - -
412B ASN* 4.5 4.8 - - - +
413B ILE* 3.1 46.9 - - - +
416B ASN* 3.2 16.2 + - - +
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LEU* 3.1 44.6 + - + +
275B GLU* 3.8 4.7 - - - +
277B SER* 1.3 78.3 - - - +
279B GLU* 1.3 62.8 + - - +
281B THR* 3.2 24.8 + - - +
284B LEU* 4.4 10.0 - - + +
285B ASN* 4.1 8.7 - - - +
288B ILE* 4.2 18.2 - - + -
322B THR* 3.7 25.6 - - + -
326B LEU* 6.0 0.4 - - + -
360B MET* 3.5 30.7 - - + -
364B LEU* 4.1 27.4 - - + -
409B LEU* 4.5 13.9 - - + +
413B ILE* 6.2 1.1 - - + -
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLU* 3.1 11.0 + - - +
276B ASN* 3.4 25.9 - - - +
277B SER 3.0 0.2 + - - -
278B PHE* 1.3 80.6 - - - +
280B GLU* 1.3 63.4 + - + +
281B THR 3.1 4.5 + - - -
282B PRO* 3.9 10.7 - - - +
285B ASN* 5.2 5.1 + - - +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ASN* 2.9 30.2 + - - +
277B SER 2.9 4.1 + - - +
279B GLU* 1.3 81.3 - - + +
281B THR* 1.3 55.9 + - - +
282B PRO* 3.5 7.3 - - - +
408B LYS* 5.2 3.1 - - - +
412B ASN* 2.8 29.7 + - - +
415B LYS* 3.0 29.2 + - - +
416B ASN* 3.2 30.8 + - - +
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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
------------------------------------------------------------
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