Contacts of the helix formed by residues 297 - 317 (chain B) in PDB entry 3QEK
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 ASN 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B THR* 5.1 0.2 - - - -
294B ASN* 2.9 34.0 + - - +
295B GLY 3.5 0.6 - - - -
296B LYS* 1.3 76.4 - - - +
298B GLU* 1.3 60.8 + - - +
299B SER* 3.3 8.1 + - - -
300B ALA* 3.0 25.3 + - + -
301B HIS* 3.2 17.9 + - - -
502B NAG 1.4 75.2 + - + +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.5 8.7 - - - +
34B SER* 2.6 46.1 + - - -
38B HIS* 3.4 33.0 + - + +
93B SER* 3.2 26.1 + - - -
95B PRO* 4.2 4.0 - - - +
121B LEU* 4.7 2.9 - - + +
122B THR* 4.5 15.0 - - + +
296B LYS 3.2 8.6 + - - +
297B ASN* 1.3 72.6 - - - +
299B SER* 1.3 57.8 + - - +
301B HIS* 3.3 3.2 + - - +
302B ILE* 2.9 42.7 + - + +
502B NAG 5.3 0.8 - - - +
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B HIS* 4.1 10.6 + - - -
41B ILE* 3.2 35.0 - - - +
297B ASN* 3.1 9.3 + - - -
298B GLU* 1.3 80.9 - - - +
300B ALA* 1.3 61.8 + - - +
302B ILE* 3.4 7.0 + - - +
303B SER* 3.2 24.8 + - - -
502B NAG 5.2 5.2 - - - -
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASN* 4.8 2.7 - - - +
297B ASN* 3.0 34.2 + - + +
299B SER* 1.3 76.1 - - - +
301B HIS* 1.3 62.0 + - - +
303B SER* 3.4 6.3 + - - -
304B ASP* 3.2 27.2 + - - -
355B VAL* 4.1 16.4 - - + +
356B THR* 3.9 20.9 - - + -
502B NAG 3.9 10.3 - - - +
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Residues in contact with HIS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.5 29.6 + - + +
122B THR* 4.8 2.7 - - + -
140B THR* 2.9 45.8 + - - +
141B VAL* 3.3 18.9 - - + +
293B ILE 5.2 0.8 + - - -
294B ASN* 3.1 30.4 + - - +
295B GLY 4.8 0.2 - - - -
297B ASN 3.2 21.4 + - - +
298B GLU* 4.0 3.6 - - - +
299B SER 3.2 0.2 - - - -
300B ALA* 1.3 75.8 - - - +
302B ILE* 1.3 59.2 + - - +
304B ASP* 4.5 4.2 - - - +
305B ALA* 2.8 34.7 + - - +
356B THR* 3.8 21.9 + - + +
367B ARG* 4.2 3.6 + - - -
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.8 15.3 - - + -
38B HIS* 3.6 42.2 - - + +
41B ILE* 4.1 9.6 - - + +
42B PHE* 3.5 40.4 - - + +
45B ALA* 4.6 1.8 - - + -
91B LEU* 4.6 3.4 - - + -
121B LEU* 3.7 22.6 - - + +
298B GLU* 2.9 26.3 + - + +
299B SER* 3.7 7.0 - - - +
301B HIS* 1.3 76.5 - - - +
303B SER* 1.3 63.3 + - - +
305B ALA* 3.9 0.7 - - - +
306B VAL* 3.1 25.3 + - - +
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.4 10.6 - - - +
45B ALA* 4.3 15.8 - - - +
299B SER* 3.2 12.8 + - - -
300B ALA* 3.6 9.1 - - - -
301B HIS 3.2 0.4 - - - -
302B ILE* 1.3 80.8 - - - +
304B ASP* 1.3 62.1 + - - +
306B VAL* 3.5 2.8 + - - +
307B ALA* 3.1 21.8 + - - +
355B VAL* 4.5 16.2 - - - -
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Residues in contact with ASP 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 5.4 5.4 - - + -
300B ALA 3.2 12.1 + - - +
301B HIS* 4.1 5.8 - - - +
303B SER* 1.3 74.3 - - - +
305B ALA* 1.3 60.2 + - - +
307B ALA* 3.2 6.0 + - - +
308B VAL* 2.9 33.7 + - - +
351B TYR* 5.0 2.1 - - - -
354B GLY* 3.4 5.7 - - - -
355B VAL* 2.8 29.4 + - - +
356B THR* 2.6 43.1 + - - +
359B ILE* 3.5 22.2 - - + +
367B ARG* 5.9 0.2 - - - +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.7 18.2 - - + -
119B ILE* 4.5 6.5 - - + -
121B LEU* 3.5 23.1 - - + -
140B THR* 4.4 15.6 - - + +
301B HIS 2.8 23.7 + - - +
304B ASP* 1.3 71.7 - - - +
306B VAL* 1.3 57.7 + - - +
308B VAL* 3.3 6.0 + - - +
309B VAL* 2.8 35.3 + - + +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 5.2 5.2 - - + -
42B PHE* 3.6 36.8 - - + -
45B ALA* 3.6 37.2 - - + +
46B VAL* 3.9 14.1 - - + +
49B ALA* 4.2 8.1 - - + -
60B LEU* 5.6 2.5 - - + -
91B LEU* 3.9 6.3 - - + -
302B ILE 3.1 18.4 + - - +
303B SER 3.9 4.3 - - - +
305B ALA* 1.3 75.3 - - - +
307B ALA* 1.3 56.2 + - - +
309B VAL* 3.3 7.3 + - + +
310B ALA* 2.8 29.6 + - + +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 5.4 3.6 - - - -
53B HIS* 5.2 1.2 + - - -
303B SER 3.1 13.6 + - - +
304B ASP* 3.2 10.1 + - - +
306B VAL* 1.3 76.4 - - - +
308B VAL* 1.3 63.1 + - - +
310B ALA* 3.4 5.4 + - - +
311B GLN* 3.1 24.6 + - - +
351B TYR* 3.5 42.5 - - + +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 5.8 2.5 - - + -
138B LEU* 5.9 0.2 - - + -
140B THR* 5.8 0.4 - - + -
304B ASP 2.9 20.7 + - - +
305B ALA* 3.6 6.1 - - - +
307B ALA* 1.3 75.5 - - - +
309B VAL* 1.3 60.1 + - + +
311B GLN* 3.4 5.5 + - - +
312B ALA* 2.9 28.2 + - - +
346B LEU* 4.2 13.0 - - + -
349B SER* 4.2 17.7 + - - -
351B TYR* 4.0 13.7 - - + +
359B ILE* 3.5 37.5 - - + -
361B PHE* 3.8 25.8 - - + -
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 3.4 39.9 - - + -
89B ALA* 4.7 5.2 - - + -
91B LEU* 4.2 10.1 - - + -
119B ILE* 3.4 32.5 - - + -
305B ALA 2.8 22.1 + - - +
306B VAL* 3.7 7.0 - - + +
308B VAL* 1.3 76.1 - - + +
310B ALA* 1.3 59.2 + - - +
312B ALA* 3.3 1.2 + - - +
313B ILE* 2.8 34.9 + - + +
342B PHE* 4.4 7.4 - - + -
346B LEU* 3.9 11.7 - - + -
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.7 17.7 - - + -
53B HIS* 4.1 12.3 - - + +
60B LEU* 3.5 31.4 - - + +
306B VAL 2.8 18.1 + - - +
307B ALA* 3.7 4.7 - - - +
309B VAL* 1.3 76.9 - - - +
311B GLN* 1.3 63.1 + - - +
313B ILE* 3.2 4.3 + - - +
314B HIS* 3.1 30.4 + - - -
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B HIS* 3.9 22.1 + - + +
307B ALA 3.1 14.7 + - - +
308B VAL* 3.7 4.9 - - - +
310B ALA* 1.3 77.9 - - - +
312B ALA* 1.3 63.7 + - - +
314B HIS* 3.3 2.4 + - - +
315B GLU* 2.9 32.7 + - + +
349B SER* 4.1 11.3 + - - +
350B LYS 3.0 40.3 + - - +
351B TYR* 3.6 20.7 - - + -
352B PRO* 5.4 1.2 - - - +
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Residues in contact with ALA 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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308B VAL 2.9 18.1 + - - +
309B VAL 3.7 0.9 - - - +
311B GLN* 1.3 76.9 - - - +
313B ILE* 1.3 58.8 + - - +
315B GLU* 3.3 3.0 + - - -
316B LEU* 2.8 27.9 + - - +
342B PHE* 3.8 8.5 - - + -
345B VAL* 3.5 20.1 - - + +
346B LEU* 3.4 28.5 - - + -
349B SER* 3.6 16.1 + - - +
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Residues in contact with ILE 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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27B VAL* 3.6 21.1 - - + -
29B ILE* 4.4 2.2 - - + -
58B ILE* 3.5 20.2 - - + -
60B LEU* 4.2 8.3 - - + -
88B TYR* 3.6 33.4 - - + -
309B VAL* 2.8 28.8 + - + +
310B ALA* 3.2 6.7 + - - +
312B ALA* 1.3 73.4 - - - +
314B HIS* 1.3 67.3 + - - +
316B LEU* 3.1 7.3 + - + +
317B PHE* 3.0 32.8 + - + -
342B PHE* 3.5 27.1 - - + -
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Residues in contact with HIS 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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49B ALA 5.4 0.7 - - - -
50B ASN* 5.9 1.8 - - - -
53B HIS* 3.1 53.4 - + + +
58B ILE* 3.1 47.4 + - + +
60B LEU* 4.9 13.5 - - + -
310B ALA 3.1 24.8 + - - +
311B GLN 3.8 5.8 - - - +
313B ILE* 1.3 76.4 - - - +
315B GLU* 1.3 61.9 + - - +
317B PHE* 3.3 10.7 + - - +
318B GLU* 3.4 18.9 + - - +
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Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLN* 2.9 25.5 + - + +
312B ALA* 3.5 8.1 - - - +
314B HIS* 1.3 74.4 - - - +
316B LEU* 1.3 65.6 + - - +
318B GLU* 3.2 33.4 + - - +
319B MSE 4.0 8.9 - - + +
345B VAL* 4.0 25.2 - - + +
348B SER* 5.6 5.6 - - - -
349B SER* 4.9 7.8 + - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 4.6 6.7 - - + -
312B ALA 2.8 16.9 + - - +
313B ILE* 3.4 13.0 - - + +
315B GLU* 1.3 72.4 - - - +
317B PHE* 1.3 70.0 + - + +
319B MSE 3.0 44.4 + - + +
322B ILE* 3.6 46.0 - - + +
336B TRP* 4.7 1.3 - - + -
338B THR* 3.9 13.9 - - + -
341B LEU* 4.0 11.0 - - + -
342B PHE* 3.7 38.4 - - + -
345B VAL* 4.3 3.8 - - + +
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Residues in contact with PHE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 3.6 32.5 - - + -
27B VAL* 4.0 14.6 - - + -
58B ILE* 4.2 22.0 - - + -
88B TYR* 3.8 25.1 - + - -
313B ILE* 3.0 36.3 + - + +
314B HIS 3.3 5.8 + - - +
315B GLU 3.2 0.4 - - - -
316B LEU* 1.3 81.3 - - + +
318B GLU* 1.3 60.6 + - - +
319B MSE 3.2 8.6 + - - +
322B ILE* 3.8 34.1 - - + -
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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