Contacts of the helix formed by residues 13 - 32 (chain 9) in PDB entry 4N6V
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 THR 13 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840 ASN* 3.5 8.1 + - - +
850 TYR 3.7 10.3 - - - -
860 GLN* 3.3 31.2 - - + +
980 PHE* 4.6 6.7 - - + +
119 PRO 4.0 9.4 - - - +
129 ALA* 1.3 78.8 - - - +
149 ALA* 1.3 64.9 + - - +
159 GLU* 3.2 19.1 + - - +
169 THR* 2.9 17.6 + - - +
179 GLN* 3.0 21.2 + - - +
439 PHE* 4.7 8.7 - - + -
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Residues in contact with ALA 14 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840 ASN* 2.8 15.7 - - - +
850 TYR* 3.0 54.7 + - + +
860 GLN* 4.4 1.0 - - - +
139 THR* 1.3 75.5 - - - +
159 GLU* 1.3 55.5 + - - +
179 GLN* 3.3 8.1 + - - +
189 HIS* 2.9 29.5 + - - +
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Residues in contact with GLU 15 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830 SER 5.6 1.7 - - - +
840 ASN* 2.8 29.0 + - + +
980 PHE* 5.6 1.6 - - - +
139 THR* 3.1 5.5 - - - +
149 ALA* 1.3 77.0 - - - +
169 THR* 1.3 61.4 + - - +
189 HIS* 3.4 8.4 + - + +
199 ILE* 3.0 37.1 + - + +
439 PHE* 6.2 0.2 - - - -
539 TYR* 4.0 21.3 + - + -
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Residues in contact with THR 16 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129 ALA* 3.8 9.0 - - + -
139 THR* 2.9 30.8 + - - -
159 GLU* 1.3 79.1 - - - +
179 GLN* 1.3 62.0 + - - +
199 ILE* 3.2 10.0 + - + +
209 ALA* 2.9 22.3 + - - +
409 ALA* 3.8 7.4 - - + -
429 SER 4.5 0.2 - - - +
439 PHE* 3.4 35.5 - - + -
539 TYR* 6.3 0.7 - - + -
559 ILE* 3.7 31.0 - - + +
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Residues in contact with GLN 17 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139 THR 3.0 11.5 + - - +
149 ALA* 3.6 11.2 - - - +
169 THR* 1.3 77.3 - - - +
189 HIS* 1.3 58.0 + - - +
209 ALA* 3.4 4.3 + - - +
219 ASP* 2.8 63.1 + - - +
389 PHE 2.8 25.8 + - - -
399 LYS* 3.6 7.7 - - - +
409 ALA* 2.8 35.6 + - + +
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Residues in contact with HIS 18 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149 ALA 2.9 17.5 + - - +
159 GLU* 3.5 9.6 - - + +
179 GLN* 1.3 75.4 - - - +
199 ILE* 1.3 72.3 + - + +
219 ASP* 3.3 8.7 + - - +
229 GLN* 3.0 63.1 + - + +
809 LEU* 5.0 5.3 - - + +
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Residues in contact with ILE 19 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159 GLU* 3.0 35.2 + - + +
169 THR* 3.2 10.1 + - - +
189 HIS* 1.3 80.9 - - + +
209 ALA* 1.3 63.4 + - - +
229 GLN* 3.1 13.5 + - - +
239 VAL* 3.3 13.3 + - - +
539 TYR* 3.9 42.0 - - + -
559 ILE* 3.7 17.0 - - + -
699 VAL* 3.7 30.3 - - + -
719 GLN* 5.1 5.4 - - - +
809 LEU* 4.3 23.3 - - + -
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Residues in contact with ALA 20 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169 THR 2.9 15.9 + - - +
179 GLN* 3.7 8.1 - - - +
199 ILE* 1.3 77.5 - - - +
219 ASP* 1.3 63.9 + - - +
239 VAL* 3.2 11.7 + - - +
249 ARG 3.0 19.4 + - - -
389 PHE* 3.3 27.0 - - + -
409 ALA* 4.3 10.3 - - + +
559 ILE* 4.2 4.4 - - + +
579 VAL* 4.3 16.8 - - + -
679 LEU* 4.4 4.0 - - + -
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Residues in contact with ASP 21 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179 GLN* 2.8 52.3 + - - +
189 HIS* 3.6 9.0 + - - +
199 ILE 3.2 0.2 - - - -
209 ALA* 1.3 77.5 - - - +
229 GLN* 1.3 71.0 + - - +
239 VAL 3.4 0.7 + - - -
249 ARG* 3.5 26.2 + - - +
259 SER 4.8 1.0 + - - -
389 PHE* 4.2 6.9 - - - +
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Residues in contact with GLN 22 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324 ASN 5.4 2.1 - - - +
334 LYS* 5.3 11.4 - - - +
344 LYS 5.8 1.6 + - - -
189 HIS* 3.0 52.5 + - - +
199 ILE 3.1 8.5 + - - +
219 ASP* 1.3 85.5 + - - +
239 VAL* 1.3 58.5 + - - +
259 SER* 5.0 4.9 + - - -
269 GLN* 3.8 10.7 + - - -
809 LEU* 3.6 25.5 - - + +
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Residues in contact with VAL 23 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199 ILE 3.3 9.4 + - - +
209 ALA* 3.4 11.4 - - - +
229 GLN* 1.3 77.2 - - - +
249 ARG* 1.3 66.6 + - - +
259 SER 3.2 2.9 - - - -
269 GLN* 2.9 35.1 + - - +
279 LEU* 3.1 11.1 + - + +
389 PHE* 5.1 0.2 - - + -
679 LEU* 3.7 27.4 - - + -
699 VAL* 3.8 35.9 - - + -
809 LEU* 4.1 11.4 - - + +
829 LEU* 4.1 18.9 - - + +
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Residues in contact with ARG 24 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209 ALA 3.0 11.4 + - - +
219 ASP* 3.5 23.6 + - - +
239 VAL* 1.3 75.8 - - - +
259 SER* 1.3 58.8 + - - +
279 LEU* 3.1 4.4 + - - +
289 GLU* 2.8 55.6 + - + +
359 PHE* 2.8 30.9 + - - +
369 PRO 4.1 5.9 + - - -
379 VAL* 4.1 5.1 - - - +
389 PHE* 3.5 58.3 + - + +
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Residues in contact with SER 25 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344 LYS 5.2 0.7 + - - -
364 PRO* 3.5 22.6 - - - +
374 VAL* 5.5 3.4 - - - +
219 ASP 4.8 1.2 + - - -
229 GLN 5.0 4.5 + - - -
239 VAL 3.2 1.3 - - - -
249 ARG* 1.3 79.7 - - - +
269 GLN* 1.3 59.4 + - - +
289 GLU* 3.7 15.8 - - - +
299 GLU* 2.9 32.9 + - - +
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Residues in contact with GLN 26 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344 LYS* 3.5 23.8 - - + +
364 PRO* 3.8 29.7 - - + +
229 GLN 3.8 17.6 + - - -
239 VAL* 2.9 13.6 + - - +
259 SER* 1.3 78.1 + - - +
279 LEU* 1.3 61.7 + - - +
299 GLU* 3.9 1.6 - - - +
309 LYS* 3.0 29.3 + - + +
809 LEU 3.2 22.8 + - - -
819 THR* 3.5 10.0 - - - +
829 LEU* 2.8 40.1 + - + +
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Residues in contact with LEU 27 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239 VAL 3.1 8.7 + - - +
249 ARG* 3.6 7.9 - - - +
269 GLN* 1.3 75.2 - - - +
289 GLU* 1.3 53.9 + - - +
309 LYS* 3.1 3.7 + - - -
319 GLU* 2.7 40.3 + - + +
359 PHE* 3.6 29.6 - - + -
389 PHE* 3.6 22.9 - - + -
659 VAL* 4.0 20.2 - - + -
679 LEU* 4.0 5.4 - - + -
829 LEU* 3.7 13.4 - - + +
859 TYR* 3.5 50.3 - - + -
879 THR* 5.1 0.7 - - + -
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Residues in contact with GLU 28 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614 ASP* 5.8 0.2 - - - +
249 ARG* 2.8 49.0 + - - +
259 SER* 3.7 19.5 + - - +
279 LEU* 1.3 70.6 - - - +
299 GLU* 1.3 54.2 + - - +
319 GLU* 4.8 0.7 - - - -
329 ASN* 2.7 32.7 + - - -
339 LYS 3.1 27.9 + - - +
349 LYS* 3.9 23.3 + - + +
359 PHE* 3.6 29.6 + - + -
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Residues in contact with GLU 29 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364 PRO* 3.7 29.1 - - + +
374 VAL* 3.4 26.8 - - + +
259 SER 2.9 18.7 + - - +
269 GLN 3.9 3.1 - - - +
289 GLU* 1.3 77.6 - - - +
309 LYS* 1.3 62.8 + - + +
329 ASN* 3.5 12.7 + - - +
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Residues in contact with LYS 30 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638 ASP* 6.0 1.6 - - - -
888 ASN* 3.1 25.6 + - - +
269 GLN* 3.0 22.2 + - + +
279 LEU 3.7 3.6 - - - +
299 GLU* 1.3 76.2 - - + +
319 GLU* 1.3 61.7 + - - +
329 ASN* 3.6 1.4 + - - +
829 LEU* 5.4 6.5 - - + +
849 ASN* 6.3 0.6 - - - +
859 TYR* 3.5 35.3 + - + +
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Residues in contact with GLU 31 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318 GLU* 4.3 13.2 - - - +
338 LYS* 4.3 21.9 + - - +
878 THR* 4.4 7.7 + - - -
888 ASN* 5.0 1.2 + - - +
279 LEU* 2.7 30.6 + - + +
289 GLU 4.2 0.7 - - - +
309 LYS* 1.3 72.6 - - - +
329 ASN* 1.3 70.1 + - - +
339 LYS* 3.2 33.1 + - + +
359 PHE* 4.4 7.9 - - + -
859 TYR* 2.6 42.0 + - + +
879 THR* 3.8 17.4 + - + +
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Residues in contact with ASN 32 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338 LYS* 5.6 3.4 - - - +
289 GLU 2.7 15.1 + - - -
299 GLU* 3.5 11.0 + - - +
309 LYS 3.4 4.3 - - - +
319 GLU* 1.3 77.0 - - - +
339 LYS* 1.3 57.8 + - - +
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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