Contacts of the helix formed by residues 9 - 26 (chain 4) 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 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533 THR* 4.2 4.9 - - - -
84 ARG* 1.3 76.7 - - - +
104 TYR* 1.3 65.4 + - - +
114 SER* 2.7 28.3 + - - -
124 GLN* 2.8 24.5 + - - +
134 ARG* 3.0 20.7 + - - +
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Residues in contact with TYR 10 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453 PHE* 5.1 0.7 - + - -
463 GLN* 5.2 14.5 + - - +
493 VAL* 4.6 6.5 - - + -
503 PRO* 3.7 40.2 - - + -
533 THR* 3.1 39.5 - - + +
94 SER* 1.3 75.7 - - - +
114 SER* 1.3 76.7 + - - +
134 ARG* 3.4 6.0 - - - +
144 TYR* 2.8 51.2 + + + -
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Residues in contact with SER 11 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94 SER* 2.7 21.7 + - - -
104 TYR* 1.3 104.3 - - - +
124 GLN* 1.3 58.3 + - - +
144 TYR* 3.9 3.8 - - - +
154 ALA* 2.9 28.9 + - - +
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Residues in contact with GLN 12 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 SER 4.7 1.9 + - - +
84 ARG* 3.6 26.9 - - - +
94 SER* 2.8 39.2 + - - +
104 TYR 3.1 0.4 - - - -
114 SER* 1.3 84.5 + - - +
134 ARG* 1.3 64.8 + - - +
154 ALA* 3.7 5.2 - - - +
164 LYS* 3.1 25.3 + - - +
405 VAL* 5.0 1.9 - - - +
435 GLN* 5.3 7.4 - - + +
445 ASN* 2.9 33.0 + - - +
475 THR* 4.9 15.4 + - - +
485 ASN* 5.5 3.0 - - - +
3378 A 4.1 3.5 + - - -
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Residues in contact with ARG 13 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453 PHE* 4.5 7.9 - - + -
493 VAL* 3.8 20.1 + - + +
523 PHE* 4.5 4.4 - - - +
533 THR* 2.7 48.6 + - - +
563 ASN* 4.0 11.6 - - - +
84 ARG* 4.3 7.9 - - + -
94 SER 3.0 20.3 + - - +
104 TYR* 3.4 7.2 - - + +
124 GLN* 1.3 76.4 - - - +
144 TYR* 1.3 57.6 + - - +
174 TRP* 3.0 29.6 + - - +
137 A 3.9 14.6 + - - -
147 T 4.8 5.1 + - - -
3368 T 3.8 30.8 + - + +
3378 A 3.6 57.3 + - - +
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Residues in contact with TYR 14 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423 GLN* 3.9 9.9 + - - +
453 PHE* 3.5 33.8 - + + -
463 GLN* 3.4 41.5 + - + -
104 TYR* 2.8 34.6 + + + +
114 SER* 3.9 4.3 - - - +
134 ARG* 1.3 75.5 - - - +
154 ALA* 1.3 71.3 + - - +
174 TRP* 3.0 15.2 + + - +
184 GLN* 2.7 58.7 + - + +
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Residues in contact with ALA 15 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114 SER 2.9 20.9 + - - +
124 GLN* 3.3 7.4 + - - +
144 TYR* 1.3 83.7 - - + +
164 LYS* 1.3 61.3 + - - +
184 GLN* 3.3 5.7 + - - +
194 ALA* 3.1 19.8 + - - +
405 VAL* 4.1 23.3 - - + +
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Residues in contact with LYS 16 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124 GLN 3.1 12.4 + - - +
154 ALA* 1.3 77.6 - - - +
174 TRP* 1.3 66.3 + - - +
194 ALA* 3.1 4.7 + - - +
204 LYS* 3.0 26.0 + - + +
375 VAL* 4.7 8.1 - - + -
405 VAL* 3.9 19.7 - - + +
445 ASN* 5.5 2.7 - - - +
47 T 3.7 33.8 + - - +
57 A 2.8 31.7 + - - -
3368 T 3.3 33.0 + - - +
3378 A 3.9 22.6 + - - +
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Residues in contact with TRP 17 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413 ALA* 4.1 20.9 - - + -
423 GLN* 4.2 6.5 - - + -
453 PHE* 3.5 54.7 - + + -
134 ARG 3.0 20.5 + - - +
144 TYR* 3.4 15.3 - + - +
164 LYS* 1.3 76.7 - - - +
184 GLN* 1.3 94.0 + - - +
204 LYS* 3.4 2.7 + - - +
214 PHE* 2.9 52.9 + + + +
157 A 3.8 34.2 + - + -
3358 A 3.8 26.9 + - + -
3368 T 3.8 19.4 - - - +
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Residues in contact with GLN 18 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423 GLN* 3.2 39.5 - - - +
144 TYR* 2.7 58.9 + - + +
154 ALA* 3.5 6.7 - - - +
174 TRP* 1.3 83.6 - - - +
194 ALA* 1.3 62.2 + - - +
214 PHE* 3.2 5.5 + - - +
224 ASN* 2.9 64.2 + - - +
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Residues in contact with ALA 19 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154 ALA 3.1 9.4 + - - +
164 LYS* 3.1 10.6 + - - +
184 GLN* 1.3 80.0 - - - +
204 LYS* 1.3 59.5 + - - +
224 ASN* 3.5 9.7 + - - +
234 ALA* 3.0 25.8 + - - +
365 ASN* 3.4 35.0 - - - +
375 VAL* 3.7 16.4 - - + -
405 VAL* 4.5 4.7 - - + -
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Residues in contact with LYS 20 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164 LYS* 3.0 21.4 + - + +
174 TRP 3.9 3.1 - - - +
194 ALA* 1.3 74.5 - - - +
214 PHE* 1.3 66.0 + - - +
234 ALA* 3.3 4.3 + - + +
244 PHE* 3.0 24.4 + - - +
335 ILE* 3.9 19.5 - - + -
375 VAL* 3.6 16.4 - - + -
57 A 2.8 31.6 + - - +
67 T 3.1 24.9 + - - -
3358 A 3.4 43.3 + - + +
3368 T 3.2 20.9 + - - +
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Residues in contact with PHE 21 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343 LEU* 3.9 29.8 - - + -
373 VAL* 4.5 5.2 - - + -
383 SER* 3.5 37.5 - - - -
413 ALA* 4.5 9.4 - - + -
423 GLN* 5.8 0.2 - - + -
174 TRP* 2.9 49.7 + + + +
184 GLN* 3.6 12.3 - - - +
204 LYS* 1.3 76.4 - - - +
224 ASN* 1.3 72.5 + - - +
244 PHE* 3.3 12.6 + + - +
254 SER* 3.0 22.9 + - - -
157 A 5.7 3.1 - + - -
167 T 4.5 24.5 - - + -
3348 T 6.0 1.8 - - - -
3358 A 5.2 2.8 - - - -
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Residues in contact with ASN 22 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383 SER* 5.5 2.3 + - - -
423 GLN* 4.6 3.5 + - - -
184 GLN* 2.9 50.6 + - - +
194 ALA* 3.5 9.1 - - - +
214 PHE* 1.3 81.4 - - - +
234 ALA* 1.3 62.9 + - - +
254 SER* 2.6 26.3 + - - -
264 ASN* 3.6 3.8 + - - +
325 THR* 5.2 0.2 - - - +
365 ASN* 4.0 11.7 - - - +
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Residues in contact with ALA 23 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194 ALA 3.0 13.8 + - - +
204 LYS* 3.5 9.9 - - + +
214 PHE 3.2 0.2 - - - -
224 ASN* 1.3 79.1 - - - +
244 PHE* 1.3 62.3 + - - +
264 ASN* 3.1 22.0 + - - +
294 VAL* 3.3 11.4 - - + +
325 THR* 3.6 14.4 - - + -
335 ILE* 3.8 27.6 - - + -
365 ASN* 3.5 16.6 - - - +
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Residues in contact with PHE 24 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243 PHE* 4.4 9.6 - + - -
343 LEU* 3.5 30.3 - - + -
204 LYS 3.0 18.0 + - - +
214 PHE* 3.7 11.4 - + - +
234 ALA* 1.3 76.6 - - - +
254 SER* 1.3 62.4 + - - +
264 ASN 3.0 1.4 + - - -
294 VAL* 3.8 5.6 - - - -
304 ALA* 3.3 45.5 + - - +
334 ILE* 4.2 19.1 - - + -
344 LEU* 4.0 25.8 - - + -
177 A 6.0 0.4 - - - -
3348 T 3.7 51.6 - - + +
3358 A 5.4 2.7 - - - +
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Residues in contact with SER 25 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313 SER* 3.4 21.7 - - - +
343 LEU* 3.8 38.1 - - - -
353 SER* 4.5 6.6 - - - -
383 SER* 4.7 7.3 + - - -
214 PHE* 3.0 14.8 + - - -
224 ASN* 2.6 23.3 + - - -
244 PHE* 1.3 75.9 - - - +
264 ASN* 1.3 61.0 + - - +
274 PRO* 3.2 4.0 - - - +
304 ALA* 4.9 0.7 - - - -
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Residues in contact with ASN 26 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224 ASN 4.5 2.5 - - - +
234 ALA 3.1 15.1 + - - +
244 PHE 3.0 1.2 + - - -
254 SER* 1.3 77.9 + - - +
274 PRO* 1.4 68.2 - - - +
284 THR* 2.9 24.4 + - - -
294 VAL* 2.7 37.5 + - + -
304 ALA* 2.8 11.5 + - - -
325 THR* 4.0 18.7 + - + +
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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