Contacts of the helix formed by residues 9 - 26 (chain 6) in PDB entry 3J9X
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 SER 9 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535 THR* 4.2 5.4 - - - -
86 ARG* 1.3 75.4 - - - +
106 TYR* 1.3 65.8 + - - +
116 SER* 2.7 27.9 + - - -
126 GLN* 2.8 24.1 + - - +
136 ARG* 3.0 20.8 + - - +
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Residues in contact with TYR 10 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455 PHE* 5.1 0.7 - + - -
465 GLN* 5.2 14.0 + - + +
495 VAL* 4.6 6.7 - - + -
505 PRO* 3.7 41.9 - - + +
535 THR* 3.1 38.4 - - + +
96 SER* 1.3 75.6 - - - +
116 SER* 1.3 77.1 + - - +
136 ARG* 3.4 6.8 - - - +
146 TYR* 2.8 49.4 + + + +
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Residues in contact with SER 11 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 SER* 2.7 21.7 + - - -
106 TYR* 1.3 102.9 - - - +
126 GLN* 1.3 59.1 + - - +
146 TYR* 3.9 3.7 - - - +
156 ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 12 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76 SER 4.7 1.9 + - - +
86 ARG* 3.6 34.9 - - - +
96 SER* 2.8 38.2 + - - +
106 TYR 3.1 0.2 - - - -
116 SER* 1.3 83.3 + - - +
136 ARG* 1.3 65.8 + - - +
156 ALA* 3.7 6.2 - - - +
166 LYS* 3.1 25.3 + - - +
3488 T 4.7 0.6 - - - +
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Residues in contact with ARG 13 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455 PHE* 4.5 8.8 - - + -
495 VAL* 3.8 19.0 + - + +
525 PHE* 4.5 4.6 - - - +
535 THR* 2.7 49.0 + - - +
565 ASN* 4.0 16.2 - - - +
86 ARG* 4.3 18.4 - - + -
96 SER 3.0 19.3 + - - +
106 TYR* 3.2 6.9 + - + +
126 GLN* 1.3 78.2 - - - +
146 TYR* 1.3 56.8 + - - +
176 TRP* 3.0 29.7 + - - +
17 A 3.9 18.6 + - - -
27 T 4.8 5.5 + - - -
3488 T 3.8 48.2 + - + +
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Residues in contact with TYR 14 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425 GLN* 3.9 10.5 + - - +
455 PHE* 3.5 33.8 - + + -
465 GLN* 3.4 40.3 + - + -
106 TYR* 2.8 34.7 + + + +
116 SER* 3.9 4.3 - - - +
136 ARG* 1.3 74.9 - - - +
156 ALA* 1.3 71.3 + - - +
176 TRP* 3.0 15.0 + + - +
186 GLN* 2.7 58.7 + - + +
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Residues in contact with ALA 15 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 SER 2.9 21.5 + - - +
126 GLN* 3.7 7.6 - - - +
146 TYR* 1.3 83.5 - - + +
166 LYS* 1.3 63.0 + - - +
186 GLN* 3.3 5.4 + - - +
196 ALA* 3.1 19.2 + - - +
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Residues in contact with LYS 16 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126 GLN 3.1 13.9 + - - +
156 ALA* 1.3 76.4 - - - +
176 TRP* 1.3 67.3 + - - +
196 ALA* 3.1 8.6 + - + +
206 LYS* 3.0 32.8 + - + +
3488 T 3.3 44.8 + - - +
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Residues in contact with TRP 17 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415 ALA* 4.1 20.2 - - + -
425 GLN* 4.2 7.0 - - + -
455 PHE* 3.5 55.8 - + + -
136 ARG 3.0 21.2 + - - +
146 TYR* 3.4 14.8 - + - +
166 LYS* 1.3 76.8 - - - +
186 GLN* 1.3 92.4 + - - +
206 LYS* 3.4 2.5 + - - +
216 PHE* 2.8 53.9 + + + +
37 A 3.8 34.0 + - + -
3478 A 3.8 26.9 + - + -
3488 T 3.8 19.2 - - - +
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Residues in contact with GLN 18 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425 GLN* 3.2 39.8 - - - +
146 TYR* 2.7 57.2 + - + +
156 ALA* 3.5 6.7 - - - +
176 TRP* 1.3 82.3 - - - +
196 ALA* 1.3 63.5 + - - +
216 PHE* 3.2 6.3 + - - +
226 ASN* 2.9 63.2 + - - +
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Residues in contact with ALA 19 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 ALA 3.1 9.9 + - - +
166 LYS* 3.1 13.3 + - + +
186 GLN* 1.3 78.9 - - - +
206 LYS* 1.3 62.0 + - + +
226 ASN* 3.5 10.0 + - - +
236 ALA* 3.0 26.5 + - - +
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Residues in contact with LYS 20 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166 LYS* 3.0 30.9 + - + +
176 TRP 3.9 2.7 - - - +
196 ALA* 1.3 76.3 - - + +
216 PHE* 1.3 65.7 + - - +
236 ALA* 3.3 10.5 + - + +
246 PHE* 3.0 25.3 + - - +
3478 A 3.4 54.1 + - + +
3488 T 3.2 23.8 + - - +
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Residues in contact with PHE 21 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345 LEU* 3.9 30.7 - - + -
375 VAL* 4.5 5.4 - - + -
385 SER* 3.5 37.9 - - - -
415 ALA* 4.5 9.6 - - + -
425 GLN* 5.6 0.4 - - + -
176 TRP* 2.8 49.7 + + + +
186 GLN* 3.6 12.1 - - - +
206 LYS* 1.3 78.6 - - - +
226 ASN* 1.3 71.0 - - - +
246 PHE* 3.3 11.3 + + - +
256 SER* 3.0 22.8 + - - -
37 A 5.7 2.7 - + - -
47 T 4.5 23.3 - - - -
3468 T 6.0 2.0 - - - -
3478 A 5.2 2.6 - - - -
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Residues in contact with ASN 22 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385 SER* 5.5 1.9 + - - -
425 GLN* 4.6 3.5 + - - -
186 GLN* 2.9 51.4 + - - +
196 ALA* 3.5 8.7 - - - +
216 PHE* 1.3 79.2 - - - +
236 ALA* 1.3 63.1 + - - +
256 SER* 2.6 25.9 + - - -
266 ASN* 3.6 4.2 + - - +
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Residues in contact with ALA 23 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196 ALA 3.0 15.6 + - - +
206 LYS* 3.5 14.8 - - + +
216 PHE 3.2 0.2 - - - -
226 ASN* 1.3 78.5 - - - +
246 PHE* 1.3 63.8 + - - +
266 ASN* 3.1 22.5 + - - +
296 VAL* 3.3 18.7 - - + +
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Residues in contact with PHE 24 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245 PHE* 4.4 9.0 - + - -
345 LEU* 3.5 30.7 - - + -
206 LYS 3.0 17.0 + - - +
216 PHE* 3.7 11.9 - + - +
236 ALA* 1.3 77.8 - - - +
256 SER* 1.3 61.8 + - - +
266 ASN 3.0 1.6 + - - -
296 VAL* 3.8 5.6 - - + -
306 ALA* 3.3 44.6 + - - +
336 ILE* 4.2 19.1 - - + -
346 LEU* 4.0 25.8 - - + -
57 A 6.0 0.7 - - - -
3468 T 3.7 52.5 - - + +
3478 A 5.4 2.9 - - - +
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Residues in contact with SER 25 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315 SER* 3.4 21.1 - - - +
345 LEU* 3.8 38.6 - - - -
355 SER* 4.5 6.3 - - - -
385 SER* 4.7 7.3 + - - -
216 PHE* 3.0 14.8 + - - -
226 ASN* 2.6 23.1 + - - -
246 PHE* 1.3 76.0 - - - +
266 ASN* 1.3 61.0 + - - +
276 PRO* 3.2 4.3 - - - +
306 ALA* 4.9 0.4 - - - -
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Residues in contact with ASN 26 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226 ASN 4.5 2.0 - - - +
236 ALA* 3.1 16.4 + - - +
246 PHE 3.0 1.0 + - - -
256 SER* 1.3 79.2 + - - +
276 PRO* 1.4 68.1 - - - +
286 THR* 2.9 23.6 + - - -
296 VAL* 2.7 39.2 + - + +
306 ALA* 2.8 11.5 + - - -
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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
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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