Contacts of the helix formed by residues 289 - 306 (chain B) in PDB entry 3NA1
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 VAL 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 3.6 26.0 - - + +
167B ALA* 3.3 15.6 - - - +
168B PHE* 4.0 29.6 - - + +
171B ILE* 4.4 2.5 - - + -
195B ILE* 4.2 20.0 - - + -
198B ILE* 3.8 20.4 - - + -
285B LEU 3.3 20.0 - - - +
286B ALA 4.1 1.0 + - - -
287B GLY 3.6 1.0 - - - -
288B GLY* 1.3 77.7 - - - +
290B ASP* 1.3 68.9 + - - +
291B THR 3.2 1.9 + - - -
293B SER* 2.5 27.0 + - - -
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Residues in contact with ASP 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 3.8 15.0 - - + -
195B ILE 4.8 1.6 - - - +
198B ILE* 3.3 26.3 - - - +
199B TYR* 3.4 38.8 + - - +
202B PHE* 3.6 16.9 - - + -
286B ALA 4.9 1.2 + - - -
287B GLY 5.1 0.2 + - - -
289B VAL* 1.3 82.9 - - - +
291B THR* 1.3 62.6 + - + +
293B SER* 3.5 5.4 - - - -
294B MET* 3.2 28.8 + - - +
351B ILE* 4.2 0.2 - - - +
461B ILE* 3.6 22.6 - - + +
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 5.8 1.8 - - + -
287B GLY 2.7 29.3 + - - +
288B GLY* 3.6 6.9 + - - -
289B VAL 3.2 0.2 - - - -
290B ASP* 1.3 79.6 - - + +
292B THR* 1.3 68.6 + - - +
295B THR* 2.8 30.0 + - - -
351B ILE* 3.5 20.8 - - + +
461B ILE* 5.1 2.2 - - + -
601B HEM 3.3 38.2 - - + +
602B HCD 4.0 25.8 - - + -
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Residues in contact with THR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 3.3 5.0 - - - +
288B GLY 3.3 13.8 + - - +
291B THR* 1.3 81.9 + - - +
293B SER* 1.3 59.0 + - - +
295B THR* 3.8 1.0 - - - -
296B LEU* 2.9 37.4 + - - +
429B ALA* 3.9 19.3 - - + -
432B GLU* 3.2 35.2 + - - +
433B MET* 4.4 10.8 - - + -
601B HEM 3.6 33.0 - - + -
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 3.5 45.2 - - - +
164B PHE* 3.2 22.4 - - - -
166B PHE* 6.0 0.4 - - - -
167B ALA* 4.1 1.6 - - - -
289B VAL 2.5 25.3 + - - -
290B ASP 3.4 2.3 + - - -
292B THR* 1.3 83.6 + - - +
294B MET* 1.3 61.1 + - - +
296B LEU* 3.9 4.4 - - - +
297B GLN* 3.0 28.4 + - - +
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Residues in contact with MET 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B SER* 4.5 9.0 - - - +
163B LEU* 5.6 0.2 - - + -
164B PHE* 3.5 31.9 - - + -
290B ASP 3.2 20.6 + - - +
293B SER* 1.3 84.7 + - - +
295B THR* 1.3 60.8 + - - +
297B GLN* 3.4 31.8 + - + +
298B TRP* 3.0 38.9 + - + -
351B ILE* 3.9 13.7 - - + -
461B ILE* 4.2 4.0 - - + -
462B LEU 4.6 3.8 - - - +
463B MET* 4.0 29.4 - - + -
464B PRO* 3.8 17.0 - - - -
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B THR 2.8 22.2 + - - -
292B THR 3.8 3.4 - - - -
294B MET* 1.3 76.5 - - - +
296B LEU* 1.3 56.2 + - - +
298B TRP* 3.2 12.0 + - - +
299B HIS* 2.9 25.1 + - + +
342B ILE* 5.5 2.5 - - + -
345B THR* 3.6 15.3 - - + +
346B LEU* 3.9 32.2 - - + +
349B HIS 5.0 2.7 + - - +
351B ILE* 3.6 12.4 - - - +
433B MET* 3.5 24.5 - - + -
601B HEM 3.5 10.2 - - + +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 4.6 7.2 - - + -
166B PHE* 3.7 33.2 - - + -
292B THR 2.9 23.9 + - - +
293B SER* 3.9 4.5 - - - +
295B THR* 1.3 74.0 - - - +
297B GLN* 1.3 58.6 + - - +
299B HIS* 3.2 5.0 + - + +
300B LEU* 2.9 36.1 + - - +
432B GLU* 4.8 1.6 - - - +
433B MET* 3.6 37.0 - - + -
436B PHE* 3.5 38.1 - - + -
437B LEU* 3.9 19.7 - - + -
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASP* 4.0 5.2 - - - +
159B ILE 5.0 0.2 + - - -
160B SER* 3.4 29.8 + - - -
163B LEU* 3.6 15.0 - - + +
293B SER 3.0 19.1 + - - +
294B MET* 3.5 25.8 + - - +
295B THR 3.3 0.2 - - - -
296B LEU* 1.3 74.8 - - - +
298B TRP* 1.3 58.7 + - - +
300B LEU* 4.6 4.0 - - - -
301B TYR* 3.0 27.9 + - - +
464B PRO* 3.5 25.7 - - - +
468B ILE* 4.2 23.8 + - + +
470B PHE* 3.5 20.3 - - + -
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Residues in contact with TRP 298 (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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294B MET* 3.0 29.2 + - + +
295B THR* 3.2 9.8 + - - +
297B GLN* 1.3 72.4 - - - +
299B HIS* 1.3 61.0 + - - +
301B TYR* 3.2 26.8 + + + +
302B GLU* 2.8 33.1 + - - +
345B THR* 3.8 7.2 - - + -
349B HIS* 3.3 67.9 - + + +
350B PRO 5.9 0.4 + - - -
351B ILE* 6.0 2.0 - - + -
454B VAL* 3.9 20.0 - - + -
455B GLY 3.6 19.3 - - - -
456B THR* 4.0 12.1 - - + +
462B LEU* 4.9 3.8 + - - +
463B MET* 4.0 9.1 - - - +
464B PRO* 3.5 42.8 - - + +
468B ILE* 4.5 5.6 - - + -
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Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B THR* 2.9 13.7 + - + +
296B LEU* 3.2 11.6 + - + +
298B TRP* 1.3 71.4 - - - +
300B LEU* 1.3 66.3 + - - +
302B GLU* 3.2 4.2 + - - +
303B MET* 2.9 57.0 + - + +
313B LEU* 4.0 4.4 - - - +
338B LEU* 4.2 2.4 - - + +
341B SER* 2.9 42.3 + - - -
342B ILE* 4.2 4.0 + - - +
345B THR* 3.1 26.1 + - + +
396B PHE* 4.4 3.4 - + - -
437B LEU* 3.5 33.1 - - + +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 4.0 26.5 - - + -
163B LEU* 4.7 2.2 - - + -
296B LEU 2.9 23.9 + - - +
297B GLN* 4.6 4.0 - - - -
299B HIS* 1.3 76.4 - - - +
301B TYR* 1.3 62.8 + - - +
303B MET* 3.4 24.5 + - + +
304B ALA* 3.0 24.9 + - - +
436B PHE* 4.3 20.2 - - + -
437B LEU* 4.4 9.4 - - + -
440B MET* 4.2 19.1 - - + -
446B VAL* 4.1 22.4 - - + +
470B PHE* 3.6 22.2 - - + -
472B PHE* 4.7 2.7 - - + -
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Residues in contact with TYR 301 (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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297B GLN 3.0 19.0 + - - +
298B TRP* 3.3 28.3 - + - +
300B LEU* 1.3 76.7 - - - +
302B GLU* 1.3 81.0 + - - +
304B ALA* 3.3 5.2 + - - +
305B ARG* 3.0 50.5 + - - +
349B HIS* 4.9 0.7 - + - -
448B ILE* 3.9 13.4 - - + +
452B SER* 3.4 31.0 + - - -
453B ASP* 3.9 1.6 - - - -
454B VAL* 3.2 37.4 + - + -
468B ILE* 4.1 24.9 - - + -
470B PHE* 3.5 12.5 - - + -
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Residues in contact with GLU 302 (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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298B TRP 2.8 22.9 + - - +
299B HIS* 3.2 3.6 + - - +
301B TYR* 1.3 82.7 - - - +
303B MET* 1.3 60.4 + - - +
305B ARG* 2.7 34.0 + - - +
306B ASN* 2.9 31.5 + - - +
345B THR* 5.0 0.7 - - - +
348B LEU* 3.7 13.8 - - - +
349B HIS* 2.7 35.2 + - + +
396B PHE* 3.5 43.4 - - + +
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Residues in contact with MET 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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299B HIS* 2.9 49.1 + - + +
300B LEU* 3.7 27.6 - - + +
302B GLU* 1.3 77.6 - - - +
304B ALA* 1.3 60.9 + - - +
306B ASN 3.2 23.1 - - - +
307B LEU* 3.6 1.2 + - - -
309B VAL* 5.6 0.2 - - - -
310B GLN* 3.1 35.1 - - + +
313B LEU* 3.7 23.1 - - + -
396B PHE* 4.8 6.7 - - + -
437B LEU* 4.1 7.4 - - + -
440B MET* 5.9 1.3 - - + -
441B LEU* 3.7 33.9 - - + -
446B VAL* 5.0 6.7 - - + -
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Residues in contact with ALA 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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300B LEU 3.0 16.6 + - - +
301B TYR 3.7 4.9 - - - +
303B MET* 1.3 76.8 - - - +
305B ARG* 1.3 60.3 + - - +
307B LEU* 3.5 17.3 - - - +
310B GLN* 3.8 0.6 + - - -
446B VAL* 3.6 28.0 - - + +
447B GLU* 3.8 3.8 - - - -
448B ILE* 3.7 40.4 + - + +
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Residues in contact with ARG 305 (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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301B TYR* 3.0 45.6 + - - +
302B GLU* 2.7 39.0 + - - +
303B MET 3.2 0.2 - - - -
304B ALA* 1.3 80.4 - - - +
306B ASN* 1.3 58.8 + - - +
307B LEU* 3.9 2.0 + - - +
348B LEU* 5.1 1.0 - - - +
394B GLU* 3.2 32.1 + - - +
395B ASN* 5.1 1.4 - - - +
396B PHE* 4.6 8.5 - - - +
448B ILE* 4.2 14.4 - - + -
452B SER 4.7 5.8 - - - +
453B ASP* 4.9 8.5 + - - -
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Residues in contact with ASN 306 (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 GLU 2.9 14.4 + - - +
303B MET 3.2 6.7 - - - +
305B ARG* 1.3 79.3 - - + +
307B LEU* 1.3 62.4 + - - +
308B LYS* 3.4 11.6 + - - +
309B VAL* 3.0 40.0 + - + +
310B GLN 3.0 9.2 + - - -
395B ASN* 3.8 16.6 + - - +
396B PHE* 3.6 27.5 + - + +
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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