Contacts of the helix formed by residues 302 - 316 (chain B) in PDB entry 3Q36
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 ARG 302 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B FE 4.6 13.0 - - - -
300B HIS* 4.3 13.9 - - + +
301B LEU* 1.3 79.6 - - - +
303B HIS* 1.3 68.7 + - - +
304B GLY 3.4 2.2 - - - +
305B GLY* 3.0 5.7 + - - +
306B ARG* 3.0 19.0 + - - +
377B SER* 4.6 6.9 + - - -
378B GLN 3.2 27.6 + - - -
379B GLY* 3.3 24.9 + - - +
380B ASP* 3.4 33.3 + - - +
381B TYR* 6.3 0.4 - - - -
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Residues in contact with HIS 303 (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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302B ARG* 1.3 74.2 - - - +
304B GLY* 1.3 58.1 + - - +
306B ARG* 2.7 56.1 + - - +
307B MET* 2.8 55.7 + - + +
348B ASN* 5.3 10.5 - - - -
374B ASN* 6.1 2.0 - - - -
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Residues in contact with GLY 304 (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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302B ARG* 3.4 2.2 - - - +
303B HIS* 1.3 80.4 - - - +
305B GLY* 1.3 59.8 + - - +
307B MET* 4.0 5.7 - - - +
308B GLN* 3.2 19.6 + - - +
365B PHE* 5.5 1.0 - - - -
374B ASN* 4.4 14.6 - - - +
380B ASP* 5.2 0.4 + - - -
382B HIS* 3.4 38.3 + - - +
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Residues in contact with GLY 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 3.9 24.2 - - - -
301B LEU* 3.6 13.5 - - - -
302B ARG* 3.0 10.6 + - - +
304B GLY* 1.3 74.3 - - - +
306B ARG* 1.3 59.9 + - - +
309B TYR* 2.8 36.4 + - - +
381B TYR 5.8 1.1 - - - -
382B HIS* 3.9 7.7 + - - +
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B HIS* 4.1 6.5 + - - -
301B LEU* 2.7 52.8 + - + +
302B ARG* 3.0 13.1 + - - +
303B HIS* 2.7 51.8 + - - +
305B GLY* 1.3 72.5 - - - +
307B MET* 1.3 61.0 + - + +
310B GLY* 2.7 31.5 + - - -
327B TRP* 3.9 20.9 - - + -
331B PHE* 4.1 17.0 - - + -
345B TYR* 3.9 32.8 + - - -
349B ILE* 5.6 9.6 - - + -
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Residues in contact with MET 307 (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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303B HIS* 2.8 57.6 + - + +
304B GLY* 4.0 5.6 - - - +
306B ARG* 1.3 83.4 - - + +
308B GLN* 1.3 59.1 + - - +
311B LEU* 2.9 50.6 + - - +
348B ASN* 4.6 20.0 - - + +
352B SER* 5.1 9.0 - - - +
362B TYR* 5.4 12.6 - - - -
365B PHE* 4.2 20.0 - - + -
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Residues in contact with GLN 308 (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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287B CYS* 3.7 17.0 - - - +
288B MET* 3.6 18.9 - - + +
291B LEU* 3.7 18.9 - - + +
304B GLY 3.2 14.4 + - - +
307B MET* 1.3 78.8 - - - +
309B TYR* 1.3 63.6 + - - +
311B LEU* 4.1 1.4 - - - +
312B PHE* 3.1 24.3 + - - +
365B PHE* 4.0 24.3 + - + +
370B ILE* 3.3 26.6 - - + +
382B HIS* 3.6 5.5 - - - +
383B GLY* 2.9 41.7 + - - +
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Residues in contact with TYR 309 (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 ILE* 3.7 5.9 - - - +
284B PHE* 3.7 21.7 - + - -
288B MET* 4.1 17.3 - - - -
291B LEU* 3.9 20.8 - - + +
292B HIS* 2.6 47.0 + - + +
295B LEU* 3.8 19.7 - - + -
301B LEU* 4.2 9.0 - - + -
305B GLY 2.8 19.4 + - - +
308B GLN* 1.3 73.1 - - - +
310B GLY* 1.3 68.3 + - - +
312B PHE* 3.3 12.0 + + - +
313B LEU* 3.0 49.4 + - + +
326B PHE* 3.7 9.7 - + - -
327B TRP* 3.9 17.9 - + + -
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Residues in contact with GLY 310 (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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306B ARG 2.7 26.4 + - - -
309B TYR* 1.3 76.7 - - - +
311B LEU* 1.3 63.3 + - - +
313B LEU* 3.1 15.9 + - - +
314B LYS* 3.3 6.4 + - - +
327B TRP* 3.5 24.4 + - - -
352B SER* 6.0 2.9 - - - -
353B PHE* 5.8 2.5 - - - -
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Residues in contact with LEU 311 (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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307B MET* 2.9 33.2 + - + +
308B GLN 4.1 2.0 - - - +
310B GLY* 1.3 69.9 - - - -
312B PHE* 1.3 65.5 + - - +
314B LYS* 2.9 22.4 + - - +
315B GLY 2.9 18.4 + - - -
352B SER* 4.4 19.7 - - - +
362B TYR* 3.7 28.0 - - + +
363B THR 4.0 8.3 - - - +
364B PRO* 3.3 21.6 - - + +
365B PHE* 3.1 43.3 - - + +
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Residues in contact with PHE 312 (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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284B PHE* 3.9 27.1 - + - -
285B PRO* 4.0 12.8 - - + -
288B MET* 3.5 51.8 - - + -
308B GLN 3.1 18.8 + - - +
309B TYR* 3.5 15.5 - + - +
311B LEU* 1.3 77.4 - - - +
313B LEU* 1.3 66.1 + - + +
315B GLY 3.1 4.3 + - - -
316B ILE* 3.2 21.7 + - + +
364B PRO* 4.3 1.8 - - - +
365B PHE 5.4 0.9 - - - +
444B PRO* 3.6 24.7 - - + -
445B ASN* 3.1 50.2 + - - +
448B PHE* 4.2 8.3 - - + -
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Residues in contact with LEU 313 (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 ILE* 4.4 10.3 - - + -
284B PHE* 4.4 5.4 - - + -
309B TYR* 3.0 50.9 + - + +
310B GLY 3.1 7.6 + - - +
312B PHE* 1.3 76.8 - - + +
314B LYS* 1.3 63.3 + - - +
316B ILE* 2.8 42.5 + - + +
318B LEU* 3.3 28.7 + - + +
323B ALA* 6.3 1.8 - - + -
326B PHE* 3.4 38.4 - - + -
327B TRP* 4.5 10.8 - - + +
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Residues in contact with LYS 314 (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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310B GLY 3.3 6.0 + - - +
311B LEU* 2.9 17.4 + - - +
313B LEU* 1.3 77.8 - - - +
315B GLY* 1.3 57.4 + - - +
317B GLY* 3.0 21.3 + - - -
318B LEU* 3.8 12.7 + - - +
352B SER* 2.9 29.4 + - - +
353B PHE* 3.6 43.7 - - + -
362B TYR 3.3 24.2 + - - -
363B THR* 4.8 0.4 - - - +
364B PRO* 4.0 24.4 - - - +
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Residues in contact with GLY 315 (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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311B LEU 2.9 12.4 + - - -
312B PHE 3.4 5.4 - - - -
313B LEU 3.1 0.4 - - - -
314B LYS* 1.3 79.3 - - - +
316B ILE* 1.3 59.4 + - - +
317B GLY* 3.1 1.3 + - - -
364B PRO* 3.9 13.9 - - - +
445B ASN* 3.6 17.5 + - - +
449B CYS* 5.7 4.0 - - - -
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Residues in contact with ILE 316 (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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271B ILE* 3.1 39.5 + - + +
276B ILE* 5.3 4.9 - - + -
279B LEU* 5.3 1.6 - - + -
284B PHE* 4.1 17.3 - - + -
312B PHE* 3.2 18.1 + - + +
313B LEU* 2.8 48.2 - - + +
315B GLY* 1.3 74.4 - - - +
317B GLY* 1.3 56.6 + - - +
318B LEU* 4.5 8.7 - - + +
445B ASN* 3.7 10.8 - - - +
448B PHE* 3.3 35.9 - - + -
449B CYS* 6.2 2.2 - - - -
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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