Contacts of the helix formed by residues 9 - 26 (chain 1) 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 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 ARG* 1.3 75.3 - - - +
101 TYR* 1.3 60.4 + - - +
111 SER* 3.6 9.1 + - - -
121 GLN* 2.8 35.7 + - - +
131 ARG* 2.8 27.4 + - - +
532 THR* 4.3 3.8 - - - -
47W THR* 5.5 12.9 - - - +
51W LYS* 6.0 4.9 - - - -
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Residues in contact with TYR 10 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 SER* 1.3 73.1 - - - +
111 SER* 1.3 70.7 + - - +
131 ARG* 3.0 5.6 + - + -
141 TYR* 2.9 45.4 + + + +
452 PHE* 4.1 0.9 - + - -
462 GLN* 3.3 36.0 + - - +
492 VAL* 3.8 15.9 - - + -
502 PRO* 3.5 40.2 - - + -
532 THR* 3.5 32.7 - - + +
50W PRO* 4.9 11.7 - - + -
10X TYR* 2.8 44.2 + + - -
11X SER* 5.5 0.2 - - - -
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Residues in contact with SER 11 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 SER* 3.2 9.2 + - - -
101 TYR* 1.3 87.6 - - - +
121 GLN* 1.3 60.3 + - - +
141 TYR* 4.1 3.6 - - - +
151 ALA* 3.0 30.4 + - - +
43W GLN* 5.1 8.5 - - - -
46W GLN* 2.8 48.8 + - - +
47W THR* 4.1 4.4 - - - -
50W PRO* 4.8 1.3 - - - +
10X TYR* 5.0 1.7 + - - -
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Residues in contact with GLN 12 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 SER 4.2 5.7 + - - +
81 ARG* 3.6 29.4 - - - +
91 SER* 2.8 40.1 + - - +
111 SER* 1.3 77.2 - - - +
131 ARG* 1.3 67.1 + - - +
151 ALA* 3.7 5.6 - - - +
161 LYS* 3.2 24.1 + - - +
327 T 4.5 3.2 + - - -
43W GLN* 6.1 2.2 - - - +
40z VAL* 5.2 1.7 - - - +
43z GLN* 5.3 9.1 - - + +
44z ASN* 2.9 33.9 + - - +
47z THR* 4.6 19.1 + - - +
48z ASN* 5.2 1.6 - - - +
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Residues in contact with ARG 13 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 ARG* 4.1 6.7 - - + +
91 SER 2.8 23.5 + - - +
101 TYR* 3.0 10.3 + - + +
121 GLN* 1.3 72.6 - - - +
141 TYR* 1.3 62.6 + - - +
171 TRP* 3.1 23.1 + - - +
452 PHE* 4.5 8.0 - - + -
492 VAL* 3.7 20.6 + - - +
522 PHE* 4.6 4.6 - - - +
532 THR* 2.8 44.0 + - - +
562 ASN* 4.3 10.7 - - - +
317 A 3.4 54.5 + - + +
327 T 3.6 40.2 + - - -
3188 T 4.1 7.7 + - - -
3198 A 5.3 5.3 + - - -
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Residues in contact with TYR 14 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 TYR* 2.9 35.4 + + + +
111 SER* 4.1 2.9 - - - +
131 ARG* 1.3 77.8 - - - +
151 ALA* 1.3 69.4 + - - +
171 TRP* 3.1 16.1 + + - -
181 GLN* 2.7 57.3 + - + +
422 GLN* 3.7 9.0 + - - +
452 PHE* 3.4 36.3 - + + -
462 GLN* 2.9 36.9 + - + -
46W GLN* 6.2 2.2 - - - -
10X TYR* 5.5 1.8 - - - -
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Residues in contact with ALA 15 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111 SER 3.0 20.9 + - - +
121 GLN* 3.7 7.9 - - - +
141 TYR* 1.3 81.6 - - - +
161 LYS* 1.3 62.1 + - - +
181 GLN* 3.3 6.5 + - - +
191 ALA* 3.2 19.6 + - - +
40z VAL* 4.0 21.6 - - + +
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Residues in contact with LYS 16 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121 GLN 3.2 12.6 + - - +
151 ALA* 1.3 77.4 - - - +
171 TRP* 1.3 66.7 + - - +
191 ALA* 3.1 4.4 + - - +
201 LYS* 3.0 25.0 + - + +
317 A 3.3 41.8 + - - +
327 T 4.3 13.9 + - - +
3098 A 3.8 38.1 + - - +
3108 T 2.8 34.8 + - - +
37z VAL* 4.9 7.4 - - + -
40z VAL* 3.9 18.8 - - + +
44z ASN* 5.0 3.1 - - - +
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Residues in contact with TRP 17 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131 ARG 3.1 18.9 + - - +
141 TYR* 3.1 21.0 + + - +
161 LYS* 1.3 76.7 - - - +
181 GLN* 1.3 94.2 + - - +
201 LYS* 3.4 1.6 + - - +
211 PHE* 2.9 52.7 + + + +
412 ALA* 4.1 21.1 - - + -
422 GLN* 4.3 5.2 - - - -
452 PHE* 3.5 44.3 - + + -
297 A 5.3 0.2 - - - -
307 T 3.6 19.4 + - + +
317 A 3.5 28.6 - - - +
3198 A 5.0 0.2 - + - -
3208 T 2.9 37.2 + - + -
3218 A 5.4 0.2 - - - -
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Residues in contact with GLN 18 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141 TYR* 2.7 54.7 + - + +
151 ALA* 3.5 7.0 - - - +
171 TRP* 1.3 87.3 - - - +
191 ALA* 1.3 62.6 + - - +
211 PHE* 3.2 6.1 + - - -
221 ASN* 2.9 63.3 + - - +
422 GLN* 3.2 36.5 - - - +
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Residues in contact with ALA 19 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ALA 3.2 9.2 + - - +
161 LYS 3.1 9.5 + - - +
181 GLN* 1.3 79.8 - - - +
201 LYS* 1.3 58.5 + - - +
221 ASN* 3.5 8.6 + - - +
231 ALA* 3.1 26.3 + - - +
36z ASN* 3.4 35.5 - - - +
37z VAL* 3.7 17.0 - - + -
40z VAL* 4.3 7.6 - - + -
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Residues in contact with LYS 20 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 LYS* 3.0 20.6 + - + +
171 TRP 3.9 2.9 - - - +
191 ALA* 1.3 74.5 - - - +
211 PHE* 1.3 66.5 + - - +
231 ALA* 3.3 4.5 + - + +
241 PHE* 3.0 24.4 + - - +
307 T 3.5 40.4 + - + +
317 A 3.1 30.2 + - - +
3108 T 2.8 33.0 + - - +
3118 A 3.2 27.6 + - - -
33z ILE* 4.0 20.6 - - + -
37z VAL* 3.7 15.5 - - + -
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Residues in contact with PHE 21 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171 TRP* 2.9 48.1 + + + +
181 GLN* 3.6 11.2 - - - +
201 LYS* 1.3 78.1 - - - +
221 ASN* 1.3 72.7 + - - +
241 PHE* 3.3 12.0 + + - +
251 SER* 3.1 23.1 + - - -
342 LEU* 4.1 29.6 - - + -
372 VAL* 4.6 5.2 - - + -
382 SER* 3.6 37.0 - - - -
412 ALA* 4.3 11.2 - - + -
422 GLN* 5.8 0.2 - - + -
297 A 6.1 3.4 - + - -
307 T 5.6 2.4 - - - +
3208 T 5.8 0.4 - - - -
3218 A 4.5 23.6 - - - -
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Residues in contact with ASN 22 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181 GLN* 2.9 52.4 + - - +
191 ALA* 3.6 8.5 - - - +
211 PHE* 1.3 81.3 - - - +
231 ALA* 1.3 63.2 + - - +
251 SER* 2.6 26.6 + - - -
261 ASN* 3.6 3.6 + - - +
382 SER* 5.5 2.6 + - - -
422 GLN* 4.7 3.1 + - - -
32z THR* 5.2 0.2 - - - +
36z ASN* 4.0 11.0 - - - +
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Residues in contact with ALA 23 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191 ALA 3.1 11.9 + - - +
201 LYS* 3.5 11.4 - - + +
211 PHE 3.2 0.2 - - - -
221 ASN* 1.3 79.5 - - - +
241 PHE* 1.3 63.4 + - - +
261 ASN* 3.1 22.0 + - - +
291 VAL* 3.5 9.5 - - - +
32z THR* 3.6 15.2 - - + +
33z ILE* 3.8 28.3 - - + -
36z ASN* 3.4 17.2 - - - +
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Residues in contact with PHE 24 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201 LYS 3.0 17.0 + - - +
211 PHE* 3.7 12.1 - + - +
231 ALA* 1.3 77.3 - - - +
251 SER* 1.3 61.8 + - - +
261 ASN 3.0 2.0 + - - -
291 VAL* 4.0 5.8 - - - -
301 ALA* 3.3 45.1 + - + +
331 ILE* 4.3 14.4 - - + -
341 LEU* 4.0 23.3 - - + -
242 PHE* 4.4 9.2 - + - -
342 LEU* 3.4 30.1 - - + -
297 A 3.7 51.6 - - + -
307 T 4.6 8.5 - - - +
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Residues in contact with SER 25 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211 PHE* 3.1 15.2 + - - -
221 ASN* 2.6 23.2 + - - -
241 PHE* 1.3 76.3 - - - +
261 ASN* 1.3 61.6 + - - +
271 PRO* 3.2 4.5 - - - +
301 ALA* 5.0 0.4 - - - -
312 SER* 3.5 21.2 - - - +
342 LEU* 3.9 35.7 - - - -
352 SER* 4.6 6.6 - - - -
382 SER* 4.6 7.7 + - - -
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Residues in contact with ASN 26 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221 ASN 3.6 2.2 + - - +
231 ALA 3.1 15.1 + - - +
241 PHE 3.0 1.4 + - - +
251 SER* 1.3 77.2 + - - +
271 PRO* 1.4 68.2 - - - +
281 THR* 2.7 32.4 + - - +
291 VAL* 2.7 34.7 + - + -
301 ALA* 2.9 11.5 + - - -
28z THR* 4.9 3.4 - - - +
32z THR* 4.0 19.0 + - + +
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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