Contacts of the helix formed by residues 290 - 306 (chain A) in PDB entry 3N9Y
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 ASP 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PHE* 3.3 26.1 - - + -
195A ILE 4.7 1.6 - - - +
198A ILE* 3.9 12.0 - - - +
199A TYR* 3.3 39.1 + - - +
202A PHE* 3.6 16.6 - - + -
286A ALA 4.7 3.2 + - - -
287A GLY 4.6 1.2 + - - -
289A VAL* 1.3 85.9 - - - +
291A THR* 1.3 63.4 + - - +
293A SER* 3.4 7.1 + - - -
294A MET* 3.3 25.3 - - + +
351A ILE* 4.0 0.2 - - - +
461A ILE* 3.5 23.1 - - + +
463A MET* 4.1 2.8 - - + +
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Residues in contact with THR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 5.8 2.5 - - + -
287A GLY* 2.7 28.4 + - - +
288A GLY 3.8 5.4 + - - -
289A VAL 3.5 0.2 - - - -
290A ASP* 1.3 79.7 - - + +
292A THR* 1.3 69.6 + - - +
295A THR* 2.9 27.9 + - - -
351A ILE* 3.6 18.6 - - + +
461A ILE* 4.9 3.1 - - + -
601A HEM 3.3 43.7 - - + +
602A CLR 4.0 25.6 - - + -
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA* 3.4 3.3 - - - +
288A GLY 3.3 14.0 + - - -
291A THR* 1.3 82.8 + - - +
293A SER* 1.3 58.9 + - - +
295A THR* 3.8 0.7 - - - -
296A LEU* 2.8 37.7 + - - +
429A ALA* 3.8 36.1 - - + -
432A GLU* 2.8 35.6 + - - +
433A MET* 4.1 16.2 - - + -
601A HEM 4.1 13.2 - - + -
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.4 44.9 - - - +
164A PHE* 3.3 17.4 - - - -
166A PHE* 5.8 0.2 - - - -
167A ALA* 4.0 2.4 - - - +
289A VAL 2.7 26.7 + - - -
290A ASP* 3.4 6.8 + - - -
292A THR* 1.3 82.4 + - - +
294A MET* 1.3 66.1 + - - +
296A LEU* 3.8 5.0 - - - +
297A GLN* 3.1 27.0 + - - +
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A SER* 4.5 9.2 - - - +
163A LEU* 5.2 0.4 - - + -
164A PHE* 3.5 36.3 - - + -
290A ASP 3.3 19.5 + - - +
291A THR 3.5 2.5 + - - +
292A THR 3.4 0.2 - - - -
293A SER* 1.3 87.8 + - - +
295A THR* 1.3 66.0 + - - +
297A GLN* 3.4 33.0 + - + +
298A TRP* 3.0 31.8 + - + -
351A ILE* 4.3 10.1 - - + -
461A ILE* 4.8 1.8 - - + -
462A LEU 4.8 4.9 - - - +
463A MET* 3.9 24.0 - - + +
464A PRO* 3.9 19.3 - - + -
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A THR 2.9 19.2 + - - -
294A MET* 1.3 75.7 - - - +
296A LEU* 1.3 56.4 + - - +
298A TRP* 3.3 7.9 + - - -
299A HIS* 3.0 24.3 + - + +
342A ILE* 5.4 2.0 - - + -
345A THR* 3.5 20.5 - - + +
346A LEU* 3.9 25.8 - - + +
349A HIS 5.0 2.2 + - - +
351A ILE* 3.5 12.6 - - - +
433A MET* 3.6 28.3 - - + -
601A HEM 3.1 12.7 - - + +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 4.6 7.4 - - + -
166A PHE* 3.8 22.9 - - + -
292A THR* 2.8 24.2 + - - +
293A SER* 3.8 4.5 - - - +
295A THR* 1.3 73.1 - - - +
297A GLN* 1.3 66.4 + - - +
299A HIS* 3.2 4.6 + - + +
300A LEU* 2.9 30.7 + - - +
433A MET* 3.8 31.4 - - + +
436A PHE* 3.4 50.3 - - + -
437A LEU* 3.8 23.6 - - + -
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASP* 4.2 4.5 - - - +
159A ILE 4.8 0.5 + - - -
160A SER* 3.6 29.3 + - - -
163A LEU* 3.6 15.1 - - + +
293A SER 3.1 18.3 + - - +
294A MET* 3.5 23.3 - - + +
295A THR 3.3 0.2 - - - -
296A LEU* 1.3 76.5 - - - +
298A TRP* 1.3 56.8 + - + +
300A LEU* 4.6 4.3 - - - -
301A TYR* 3.0 25.6 + - - +
464A PRO* 3.5 27.7 - - + +
468A ILE* 4.1 28.4 + - + +
470A PHE* 3.5 21.2 - - + -
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Residues in contact with TRP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A MET* 3.0 29.2 + - + +
295A THR* 3.6 9.2 - - - +
296A LEU 3.2 0.4 - - - -
297A GLN* 1.3 73.4 - - - +
299A HIS* 1.3 61.6 + - - +
301A TYR* 3.2 25.9 + + + +
302A GLU* 2.8 33.8 + - - +
345A THR* 3.8 7.2 - - + -
349A HIS* 3.3 67.0 + + + +
350A PRO 5.9 0.4 + - - -
351A ILE* 6.5 0.4 - - + -
454A VAL* 3.7 21.8 - - + -
455A GLY 3.5 19.3 - - - -
456A THR* 3.8 13.4 - - + +
462A LEU 5.0 3.6 + - - -
463A MET* 4.1 6.1 - - - +
464A PRO* 3.4 44.6 - - + +
468A ILE* 4.7 3.6 - - + -
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 3.0 14.5 + - + +
296A LEU* 3.2 12.5 + - + +
298A TRP* 1.3 76.3 - - - +
300A LEU* 1.3 58.2 + - - +
302A GLU* 3.1 5.1 + - - +
303A MET* 2.8 53.3 + - + +
313A LEU* 4.1 4.2 - - - +
338A LEU* 4.3 2.2 - - + +
341A SER* 2.8 43.3 + - - -
342A ILE* 4.3 4.9 - - + +
345A THR* 3.2 25.4 + - + +
396A PHE* 4.6 3.1 - + - -
437A LEU* 3.5 44.2 - - + +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.9 27.6 - - + -
163A LEU* 4.7 2.2 - - + -
296A LEU 2.9 22.8 + - - +
297A GLN* 3.7 2.7 - - - +
299A HIS* 1.3 74.5 - - - +
301A TYR* 1.3 57.0 + - - +
303A MET* 3.4 27.2 + - + +
304A ALA* 3.0 29.6 + - - +
436A PHE* 4.4 18.4 - - + -
437A LEU* 4.3 11.2 - - + -
440A MET* 4.5 13.7 - - + -
446A VAL* 4.1 20.6 - - + +
470A PHE* 3.5 23.0 - - + -
472A PHE* 4.5 8.5 - - + -
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Residues in contact with TYR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A GLN 3.0 15.2 + - - +
298A TRP* 3.4 31.6 - + - +
300A LEU* 1.3 76.9 - - - +
302A GLU* 1.3 72.0 + - - +
304A ALA* 3.3 3.8 + - - +
305A ARG* 3.0 57.6 + - - +
349A HIS* 4.7 1.6 - + - -
448A ILE* 3.6 17.6 - - + +
451A LEU* 3.8 19.7 - - + -
452A SER 3.6 0.6 + - - -
453A ASP* 3.5 9.2 + - - +
454A VAL* 3.0 43.7 + - + -
468A ILE* 4.0 22.2 - - + -
470A PHE* 3.5 9.8 - - + -
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A TRP 2.8 23.7 + - - +
299A HIS 3.6 4.0 - - - +
301A TYR* 1.3 80.7 - - + +
303A MET* 1.3 59.9 + - - +
305A ARG* 2.8 33.1 + - - -
306A ASN* 2.6 37.4 + - - +
345A THR* 4.9 1.3 - - - +
348A LEU* 3.9 9.1 - - - +
349A HIS* 2.7 35.1 + - + +
396A PHE* 3.3 47.4 - - + +
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Residues in contact with MET 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A HIS* 2.8 51.2 + - + +
300A LEU* 3.7 28.9 - - + +
302A GLU* 1.3 73.2 - - - +
304A ALA* 1.3 61.0 + - - +
306A ASN 3.2 22.6 - - - +
307A LEU* 3.6 1.4 + - - -
310A GLN* 3.1 32.4 - - + +
313A LEU* 3.8 20.0 - - + -
396A PHE* 5.0 5.4 - - + -
437A LEU* 4.1 7.2 - - + -
440A MET* 5.9 1.3 - - + -
441A LEU* 3.7 33.4 - - + -
446A VAL* 4.5 10.1 - - + -
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU 3.0 17.7 + - - +
301A TYR 3.3 5.1 + - - +
303A MET* 1.3 75.3 - - - +
305A ARG* 1.3 60.0 + - - +
306A ASN 3.7 0.2 + - - -
307A LEU* 3.7 15.6 - - - +
310A GLN* 4.0 0.6 + - - -
446A VAL 3.7 19.5 + - - +
447A GLU* 3.8 2.3 - - - +
448A ILE* 3.7 41.1 + - + +
451A LEU* 3.7 9.5 - - - +
470A PHE* 4.6 1.8 - - + -
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A TYR* 3.0 46.9 + - - +
302A GLU* 2.8 30.2 + - - -
303A MET 3.3 0.2 - - - -
304A ALA* 1.3 76.2 - - - +
306A ASN* 1.3 82.7 + - - +
307A LEU* 3.9 1.5 + - - -
348A LEU* 5.2 1.0 - - - +
394A GLU 3.7 21.8 + - - -
395A ASN* 5.3 0.2 - - - +
396A PHE* 4.3 3.4 - - - +
451A LEU* 3.3 30.3 - - + -
452A SER 5.6 0.2 - - - -
453A ASP* 4.5 14.9 + - - -
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Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A GLU* 2.6 42.5 + - - +
303A MET 3.2 6.2 - - - +
304A ALA 3.3 0.2 - - - -
305A ARG* 1.3 101.1 + - - +
307A LEU* 1.3 60.4 + - - +
308A LYS 3.3 2.9 - - - -
309A VAL* 3.1 23.3 + - + +
310A GLN 3.0 22.3 + - - -
395A ASN* 4.0 13.7 - - - +
396A PHE* 3.6 21.2 + - + +
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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
------------------------------------------------------------
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