Contacts of the helix formed by residues 9 - 26 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531 THR* 4.2 5.4 - - - -
82 ARG* 1.3 76.3 - - - +
102 TYR* 1.3 65.3 + - - +
112 SER* 2.7 28.5 + - - -
122 GLN* 2.8 24.0 + - - +
132 ARG* 3.0 20.8 + - - +
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Residues in contact with TYR 10 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451 PHE* 5.1 0.4 - + - -
461 GLN* 5.2 14.3 + - - +
491 VAL* 4.6 7.0 - - + -
501 PRO* 3.7 40.4 - - + -
531 THR* 3.1 40.2 - - + +
92 SER* 1.3 76.7 - - - +
112 SER* 1.3 77.2 + - - +
132 ARG* 3.5 6.8 - - - +
142 TYR* 2.8 49.8 + + + -
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Residues in contact with SER 11 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 SER* 2.7 21.1 + - - -
102 TYR* 1.3 104.1 - - - +
122 GLN* 1.3 59.1 + - - +
142 TYR* 3.9 4.2 - - - +
152 ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 12 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72 SER 4.7 1.5 + - - +
82 ARG* 3.6 27.2 - - - +
92 SER* 2.8 38.5 + - - +
102 TYR 3.1 0.4 - - - -
112 SER* 1.3 84.7 + - - +
132 ARG* 1.3 64.3 + - - +
152 ALA* 3.7 5.2 - - - +
162 LYS* 3.1 26.0 + - - +
403 VAL* 5.0 2.8 - - + +
433 GLN* 5.3 7.6 - - + +
443 ASN* 2.9 32.4 + - - +
473 THR* 4.9 15.4 + - - +
483 ASN* 5.5 3.4 - - - +
3258 A 4.1 3.1 + - - -
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Residues in contact with ARG 13 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451 PHE* 4.5 7.7 - - + -
491 VAL* 3.8 19.7 + - + +
521 PHE* 4.5 4.4 - - - +
531 THR* 2.7 49.1 + - - +
561 ASN* 4.0 11.1 - - - +
82 ARG* 4.3 7.4 - - + -
92 SER 3.0 20.7 + - - +
102 TYR* 3.2 7.4 + - - +
122 GLN* 1.3 76.4 - - - +
142 TYR* 1.3 56.9 + - - +
172 TRP* 3.0 30.4 + - - +
257 A 3.9 15.2 + - - -
267 T 4.8 5.5 + - - -
3248 T 3.8 31.1 + - + +
3258 A 3.6 58.0 + - - +
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Residues in contact with TYR 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421 GLN* 3.9 9.9 + - - +
451 PHE* 3.5 34.0 - + + -
461 GLN* 3.4 40.1 + - + -
102 TYR* 2.8 35.6 + + + +
112 SER* 3.9 4.3 - - - +
132 ARG* 1.3 74.0 - - - +
152 ALA* 1.3 71.8 + - - +
172 TRP* 3.0 14.3 + + - +
182 GLN* 2.7 60.7 + - + +
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Residues in contact with ALA 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112 SER 2.9 21.1 + - - +
122 GLN* 3.3 8.0 + - - +
142 TYR* 1.3 84.3 - - + +
162 LYS* 1.3 63.2 + - - +
182 GLN* 3.3 5.4 + - - +
192 ALA* 3.1 19.6 + - - +
403 VAL* 4.1 21.7 - - + +
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Residues in contact with LYS 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122 GLN 3.1 13.3 + - - +
152 ALA* 1.3 77.6 - - - +
172 TRP* 1.3 67.3 + - - +
192 ALA* 3.1 4.9 + - - +
202 LYS* 3.0 25.3 + - + +
373 VAL* 4.7 8.5 - - + -
403 VAL* 3.9 18.3 - - + +
443 ASN* 5.5 3.4 - - - +
167 T 3.7 33.3 + - - +
177 A 2.8 32.5 + - - -
3248 T 3.3 33.5 + - - +
3258 A 3.9 22.2 + - - +
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Residues in contact with TRP 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411 ALA* 4.1 20.6 - - + -
421 GLN* 4.2 7.2 - - + -
451 PHE* 3.5 53.3 - + + -
132 ARG 3.0 20.3 + - - +
142 TYR* 3.4 15.0 - + - +
162 LYS* 1.3 77.2 - - - +
182 GLN* 1.3 93.3 + - - +
202 LYS* 3.4 2.1 + - - +
212 PHE* 2.8 52.8 + + + +
277 A 3.8 34.5 + - + -
3238 A 3.8 27.1 + - + -
3248 T 3.8 19.4 - - - +
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Residues in contact with GLN 18 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421 GLN* 3.2 40.1 - - - +
142 TYR* 2.7 56.7 + - + +
152 ALA* 3.5 6.7 - - - +
172 TRP* 1.3 82.8 - - - +
192 ALA* 1.3 62.8 + - - +
212 PHE* 3.2 5.9 + - - -
222 ASN* 2.9 62.7 + - - +
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Residues in contact with ALA 19 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152 ALA 3.1 9.4 + - - +
162 LYS* 3.1 10.8 + - - +
182 GLN* 1.3 80.1 - - - +
202 LYS* 1.3 58.9 + - - +
222 ASN* 3.5 9.7 + - - +
232 ALA* 3.0 27.0 + - - +
363 ASN* 3.4 33.5 - - - +
373 VAL* 3.7 16.6 - - + -
403 VAL* 4.5 4.5 - - + -
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Residues in contact with LYS 20 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162 LYS* 3.0 21.6 + - + +
172 TRP 3.9 3.6 - - - +
192 ALA* 1.3 74.3 - - - +
212 PHE* 1.3 66.2 + - - +
232 ALA* 3.3 4.0 + - + +
242 PHE* 3.0 24.8 + - - +
333 ILE* 3.9 19.3 - - + -
373 VAL* 3.6 17.7 - - + -
177 A 2.8 30.9 + - - +
187 T 3.1 25.1 + - - -
3238 A 3.4 45.1 + - + +
3248 T 3.2 21.1 + - - +
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Residues in contact with PHE 21 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341 LEU* 3.9 29.6 - - + -
371 VAL* 4.5 4.9 - - + -
381 SER* 3.5 37.7 - - - -
411 ALA* 4.5 9.4 - - + -
172 TRP* 2.8 49.2 + + + +
182 GLN* 3.6 12.1 - - - +
202 LYS* 1.3 76.4 - - - +
222 ASN* 1.3 71.9 - - - +
242 PHE* 3.3 11.5 + + - +
252 SER* 3.0 23.7 + - - -
277 A 5.7 2.5 - + - -
287 T 4.4 23.8 - - - -
3228 T 6.0 2.0 - - - -
3238 A 5.2 2.4 - - - -
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Residues in contact with ASN 22 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 SER* 5.5 2.4 + - - -
421 GLN* 4.6 2.8 + - - -
182 GLN* 2.9 51.9 + - - +
192 ALA* 3.5 8.3 - - - +
212 PHE* 1.3 79.9 - - - +
232 ALA* 1.3 63.2 + - - +
252 SER* 2.6 26.2 + - - -
262 ASN* 3.6 4.5 + - - +
363 ASN* 4.0 12.6 - - - +
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Residues in contact with ALA 23 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192 ALA 3.0 14.7 + - - +
202 LYS* 3.5 8.7 - - + +
212 PHE 3.2 0.2 - - - -
222 ASN* 1.3 79.0 - - - +
242 PHE* 1.3 62.8 + - - +
262 ASN* 3.1 21.7 + - - +
292 VAL* 3.3 11.3 - - - +
323 THR* 3.6 15.3 - - + -
333 ILE* 3.8 27.8 - - + -
363 ASN* 3.5 14.8 - - - +
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Residues in contact with PHE 24 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241 PHE* 4.4 9.2 - + - -
341 LEU* 3.5 30.5 - - + -
202 LYS 3.0 16.3 + - - +
212 PHE* 3.3 11.6 + + - +
232 ALA* 1.3 77.3 - - - +
252 SER* 1.3 62.7 + - - +
262 ASN 3.0 1.4 + - - -
292 VAL* 3.8 6.0 - - - +
302 ALA* 3.3 44.4 + - - +
332 ILE* 4.2 18.8 - - + -
342 LEU* 4.0 25.6 - - + -
3228 T 3.7 50.5 - - + +
3238 A 5.4 2.7 - - - -
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Residues in contact with SER 25 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311 SER* 3.4 22.2 - - - +
341 LEU* 3.8 36.6 - - - -
351 SER* 4.5 6.5 - - - -
381 SER* 4.7 7.3 + - - -
212 PHE* 3.0 15.5 + - - -
222 ASN* 2.6 23.7 + - - -
242 PHE* 1.3 75.3 - - - +
262 ASN* 1.3 62.6 + - - +
272 PRO* 3.2 4.3 - - - +
302 ALA* 4.9 0.4 - - - +
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Residues in contact with ASN 26 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 ASN 4.5 2.5 - - - +
232 ALA 3.1 15.2 + - - +
242 PHE 3.0 1.2 + - - -
252 SER* 1.3 78.2 + - - +
272 PRO* 1.4 66.5 - - - +
282 THR* 2.9 23.6 + - - -
292 VAL* 2.7 37.7 + - + -
302 ALA* 2.8 12.1 + - - -
323 THR* 4.0 19.3 + - + +
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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