Contacts of the helix formed by residues 265 - 280 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H VAL* 4.4 2.5 - - - -
247H THR 2.6 19.7 + - - +
248H ASP* 4.2 1.4 - - - +
263H ILE 3.9 0.2 + - - -
264H ASN* 1.3 69.6 - - - +
266H SER* 1.3 59.5 + - - +
267H SER* 3.2 21.8 - - - -
268H HIS* 3.2 38.0 - - + +
269H LEU* 3.0 29.7 + - - +
319H TRP* 4.5 1.6 - - - -
567H SER* 3.2 28.3 - - - +
568H SER* 3.4 17.0 - - - +
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Residues in contact with SER 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264H ASN 3.0 8.7 + - - -
265H CYS* 1.3 73.4 - - - +
267H SER* 1.3 56.8 + - - +
269H LEU* 3.7 9.4 - - - +
270H LEU* 2.9 28.9 + - - +
374H LEU* 3.8 21.1 - - - +
385H VAL* 3.4 24.9 - - - +
421H TRP* 3.7 18.3 + - - +
425H LEU* 4.8 0.7 - - - +
429H HIS* 3.7 6.2 + - - -
566H ALA 3.2 20.0 + - - -
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Residues in contact with SER 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H CYS* 3.1 12.8 - - - -
266H SER* 1.3 75.6 - - - +
268H HIS* 1.3 59.1 + - - +
270H LEU* 3.3 1.4 + - - -
271H SER* 3.0 25.5 + - - -
319H TRP* 3.3 32.2 - - - -
371H PHE* 3.3 20.7 + - - -
374H LEU* 3.9 16.8 + - - +
375H GLN* 4.1 5.2 - - - +
567H SER* 3.1 21.3 + - - -
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Residues in contact with HIS 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H ASP* 5.5 0.2 + - - -
248H ASP* 3.5 30.9 + - + +
249H ARG 5.3 2.5 - - - +
265H CYS* 3.2 34.3 - - + +
267H SER* 1.3 76.1 - - - +
269H LEU* 1.3 64.2 + - + +
271H SER* 3.4 7.8 + - - -
272H ASN* 2.8 38.0 + - - +
319H TRP* 3.6 28.2 - + - -
568H SER* 3.3 19.3 - - - -
572H GLU* 3.4 18.5 + - - -
16L G 4.0 14.0 + - + -
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Residues in contact with LEU 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H ARG* 3.4 42.0 - - + +
264H ASN* 4.4 14.8 - - + +
265H CYS 3.0 21.4 + - - +
266H SER* 3.7 6.5 - - - +
268H HIS* 1.3 76.2 - - + +
270H LEU* 1.3 57.9 + - - +
272H ASN* 2.6 29.0 + - + +
273H VAL* 2.8 15.8 + - - +
420H ILE* 4.4 5.4 - - + +
421H TRP* 3.3 40.4 - - + +
424H ASN* 3.7 27.1 - - + +
425H LEU* 4.5 2.7 - - + -
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Residues in contact with LEU 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H SER 2.9 19.5 + - - +
267H SER* 3.7 5.2 - - - +
269H LEU* 1.3 74.2 - - - +
271H SER* 1.3 62.7 + - - +
273H VAL* 3.1 18.7 - - + +
274H LEU* 3.0 17.1 + - + +
367H PHE* 3.9 31.2 - - + +
370H ILE* 3.4 35.7 - - + -
371H PHE* 3.7 29.8 - - + -
374H LEU* 5.0 1.8 - - + -
392H VAL* 4.9 2.7 - - + -
421H TRP* 4.3 25.2 - - + -
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Residues in contact with SER 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H SER 3.0 14.5 + - - -
268H HIS* 3.4 10.3 - - - -
269H LEU 3.0 0.2 - - - -
270H LEU* 1.3 75.0 - - - +
272H ASN* 1.3 64.8 + - - +
274H LEU* 2.9 10.1 + - - +
275H GLU* 2.9 32.2 + - - +
318H ARG 5.7 0.2 + - - -
319H TRP* 3.8 29.2 + - - -
320H ASN 5.8 0.9 - - - +
371H PHE* 3.7 10.2 - - - -
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Residues in contact with ASN 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H ARG* 3.2 29.1 + - - +
268H HIS* 2.8 31.7 + - - +
269H LEU* 2.6 17.6 + - - +
271H SER* 1.3 71.8 + - - +
273H VAL* 1.3 59.7 + - - +
275H GLU* 3.3 18.9 - - - +
276H ASN* 3.2 27.7 + - - +
420H ILE* 3.9 18.8 - - + +
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Residues in contact with VAL 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H LEU 2.8 13.8 + - - +
270H LEU* 3.1 26.9 - - + +
272H ASN* 1.3 72.9 - - - +
274H LEU* 1.3 57.8 + - + +
276H ASN* 3.2 4.6 + - - +
277H SER* 2.8 47.4 + - - +
367H PHE* 5.0 0.7 - - + -
413H ILE* 4.3 15.5 - - + +
416H ASN* 3.9 24.7 - - + +
417H VAL* 4.4 8.1 - - + +
420H ILE* 3.5 23.8 - - + +
421H TRP* 4.1 17.3 - - + -
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Residues in contact with LEU 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H LEU 3.0 6.9 + - - +
271H SER* 2.9 13.4 + - - +
273H VAL* 1.3 78.2 - - + +
275H GLU* 1.3 61.9 + - - +
277H SER* 3.6 7.4 + - - -
278H PHE* 2.9 52.2 + - + -
320H ASN* 3.8 26.9 - - - +
364H LEU* 4.0 8.3 - - + -
367H PHE* 3.5 42.4 - - + -
371H PHE* 3.9 20.4 - - + -
413H ILE* 5.2 4.5 - - + -
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Residues in contact with GLU 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271H SER* 2.9 20.1 + - - +
272H ASN* 3.3 24.2 - - - +
274H LEU* 1.3 74.7 - - - +
276H ASN* 1.3 80.1 + - - +
278H PHE* 2.9 8.4 + - - +
279H GLU* 2.9 24.4 + - - +
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Residues in contact with ASN 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H ASN* 3.2 13.0 + - - +
273H VAL* 3.2 4.7 + - - +
275H GLU* 1.3 91.4 - - - +
277H SER* 1.3 64.0 + - - +
278H PHE 3.1 0.2 + - - -
279H GLU* 3.1 17.2 + - - +
280H GLU* 2.8 50.9 + - - +
416H ASN* 4.2 10.8 - - - +
420H ILE* 4.8 17.0 - - + +
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Residues in contact with SER 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H VAL* 2.8 29.6 + - - +
274H LEU* 3.8 8.1 - - - -
276H ASN* 1.3 74.1 - - - +
278H PHE* 1.3 59.3 + - - +
280H GLU 3.8 1.4 - - - -
281H THR* 2.8 26.5 + - - -
409H LEU* 3.4 7.4 - - - +
412H ASN* 4.2 5.4 - - - +
413H ILE* 3.1 47.9 - - - +
416H ASN* 3.2 17.0 + - - +
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Residues in contact with PHE 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274H LEU* 2.9 43.1 + - + -
275H GLU* 2.9 9.2 + - - +
277H SER* 1.3 75.7 - - - +
279H GLU* 1.3 66.6 + - - +
280H GLU 3.0 1.8 - - - -
281H THR* 2.8 23.8 + - - +
284H LEU* 4.0 9.0 - - + -
285H ASN* 4.7 6.4 - - - +
288H ILE* 4.2 15.7 - - + -
322H THR* 4.7 16.6 - - + -
360H MET* 3.3 35.0 - - + -
364H LEU* 4.0 23.8 - - + -
409H LEU* 3.8 26.2 - - + -
413H ILE* 6.1 0.4 - - + -
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Residues in contact with GLU 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H GLU* 2.9 16.2 + - - +
276H ASN* 3.6 19.0 + - - +
278H PHE* 1.3 76.6 - - - +
280H GLU* 1.3 74.0 + - + +
281H THR 3.2 4.5 + - - -
282H PRO* 3.6 10.7 - - - +
285H ASN* 5.6 2.6 + - - -
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Residues in contact with GLU 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H ASN* 2.8 46.3 + - - +
277H SER 3.8 2.2 - - - +
279H GLU* 1.3 88.1 - - + +
281H THR* 1.3 63.1 + - - -
282H PRO* 3.5 6.8 - - - +
408H LYS* 5.3 1.9 - - - +
412H ASN* 3.6 21.4 + - - +
415H LYS* 2.9 25.3 + - - +
416H ASN* 3.3 18.4 + - - +
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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