Contacts of the helix formed by residues 269 - 285 (chain A) in PDB entry 1DJ9
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 PRO 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.3 37.0 - - + +
72A GLY* 4.7 5.2 - - - -
73A SER 4.4 2.2 - - - +
106A ILE* 5.0 2.2 - - + -
267A SER 4.3 2.0 - - - +
268A MET* 1.3 88.1 - - + +
270A PRO* 1.3 62.7 - - + +
271A ALA* 4.3 6.3 - - + +
272A GLN* 2.7 45.7 + - + +
273A ALA 3.2 6.8 + - - -
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Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.7 36.1 - - + +
71A ILE 3.4 14.8 - - - +
72A GLY 4.4 0.7 - - - +
73A SER* 3.9 17.7 - - - -
83A SER* 4.0 26.2 - - - +
85A VAL* 4.0 3.4 - - + +
86A HIS* 4.1 11.7 - - + +
268A MET 3.2 6.0 - - - +
269A PRO* 1.3 82.0 - - + +
271A ALA* 1.3 56.3 + - - +
273A ALA* 3.0 7.8 + - + +
274A GLN* 2.9 30.2 + - - +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 3.7 23.9 - - + +
65A GLY* 3.8 11.4 - - - +
66A ALA* 3.6 32.3 - - + +
69A PHE* 5.0 2.0 - - - +
70A GLY 4.6 5.5 + - - +
71A ILE* 5.5 3.4 - - + -
269A PRO* 3.0 6.5 + - + +
270A PRO* 1.3 80.4 - - - +
272A GLN* 1.3 62.6 + - - +
274A GLN* 3.4 3.2 + - - +
275A ALA* 3.1 20.3 + - - +
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 3.9 24.4 - - + -
106A ILE* 4.7 7.8 - - - +
240A VAL* 4.1 14.6 - - + -
241A SER* 2.9 41.3 + - - +
242A GLY* 4.0 1.0 + - - -
268A MET* 3.8 24.8 - - - +
269A PRO* 2.7 40.4 + - + +
271A ALA* 1.3 74.1 - - - +
273A ALA* 1.3 58.6 + - - +
275A ALA* 3.2 6.1 + - - +
276A LEU* 3.0 26.2 + - + +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.8 15.0 - - + +
86A HIS* 3.7 30.5 - - + -
89A LEU* 3.6 21.3 - - + +
268A MET* 4.0 6.9 - - - -
269A PRO 3.2 2.0 + - - -
270A PRO 3.0 10.2 + - - +
272A GLN* 1.3 78.9 - - - +
274A GLN* 1.3 63.8 + - - +
276A LEU* 3.2 0.7 + - - -
277A ARG* 3.1 27.5 + - - +
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 3.6 29.4 - - + +
65A GLY* 4.3 16.6 - - - -
68A GLN* 4.8 8.3 - - - +
69A PHE* 4.3 11.1 - - + -
85A VAL* 3.1 27.8 - - + +
270A PRO 2.9 15.7 + - - +
271A ALA 3.8 4.9 - - - +
273A ALA* 1.3 72.4 - - - +
275A ALA* 1.3 67.2 + - - +
277A ARG* 3.0 34.3 + - - +
278A ALA 3.1 17.8 + - - -
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 3.8 23.1 - - + +
61A ALA* 4.2 11.3 - - - +
62A TRP* 3.9 26.7 - - + -
240A VAL* 4.6 8.1 - - + -
271A ALA 3.1 11.0 + - - +
272A GLN 3.2 10.7 + - - +
274A GLN* 1.3 81.0 - - - +
276A LEU* 1.3 60.5 + - - +
278A ALA* 3.4 3.3 + - - +
279A SER* 3.0 21.5 + - - -
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.5 31.6 - - + -
234A PHE* 3.5 46.2 - - + -
238A PHE* 4.4 11.2 - - + -
240A VAL* 3.5 26.0 - - + -
241A SER 3.6 13.9 - - - +
268A MET* 3.8 23.6 - - + -
272A GLN* 3.0 16.5 + - + +
273A ALA 3.2 1.3 + - - +
275A ALA* 1.3 76.1 - - - +
277A ARG* 1.3 58.1 + - - +
279A SER* 3.0 7.1 + - - -
280A LEU* 2.8 29.5 + - - +
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.7 28.8 - - - +
88A ALA* 3.5 20.2 - - - +
89A LEU* 3.6 26.2 - - + +
92A GLU* 2.9 37.5 + - - +
273A ALA 3.1 9.2 + - - +
274A GLN* 3.0 36.7 + - - +
276A LEU* 1.3 76.3 - - - +
278A ALA* 1.3 56.3 + - - +
280A LEU* 3.3 6.5 + - - +
281A ALA* 2.9 28.3 + - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLN* 4.1 18.9 - - + +
58A ILE* 4.3 6.7 - - - -
61A ALA* 3.8 19.5 - - + -
274A GLN 3.1 14.6 + - - +
275A ALA 3.7 7.4 - - - +
276A LEU 3.3 0.2 - - - -
277A ARG* 1.3 74.4 - - - +
279A SER* 1.3 57.6 + - - +
281A ALA* 3.2 10.5 - - - +
282A VAL* 3.0 30.3 + - - +
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.7 8.0 - - - +
58A ILE* 3.7 17.1 - - - +
238A PHE* 2.5 46.8 + - - -
240A VAL* 4.8 2.5 - - - -
275A ALA 3.0 13.6 + - - -
276A LEU* 3.0 11.7 + - - -
278A ALA* 1.3 73.0 - - - +
280A LEU* 1.3 54.0 + - - +
282A VAL* 3.1 5.5 + - - +
283A ILE* 2.9 34.6 + - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.8 4.9 - - + -
92A GLU* 4.0 41.5 - - + +
93A LEU* 4.0 15.7 - - + +
96A TRP* 3.6 39.0 - - + -
238A PHE* 4.1 16.5 - - + -
276A LEU 2.8 15.3 + - - +
277A ARG* 3.4 10.5 - - - +
279A SER* 1.3 69.8 - - - +
281A ALA* 1.3 66.3 + - - +
283A ILE* 3.0 4.7 + - + -
284A ARG* 2.8 47.1 + - + +
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLN* 5.1 7.0 - - - +
277A ARG 2.9 13.3 + - - +
278A ALA* 3.2 14.4 - - - +
280A LEU* 1.3 76.4 - - - +
282A VAL* 1.3 63.5 + - - +
284A ARG* 3.3 6.4 + - - +
285A SER* 3.2 23.0 + - - -
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.8 26.2 - - + -
55A HIS* 3.7 27.1 - - + +
57A GLN* 3.8 18.2 - - + +
58A ILE* 4.9 2.7 - - + -
278A ALA 3.0 19.8 + - - +
279A SER* 3.1 8.0 + - - +
281A ALA* 1.3 73.7 - - - +
283A ILE* 1.3 66.0 + - - +
285A SER* 2.9 25.3 + - - -
287A GLU* 4.0 28.9 - - + +
288A GLY* 3.1 12.2 + - - +
291A ARG* 4.5 3.1 - - - -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.2 8.7 - - + -
52A LEU* 3.7 18.8 - - + -
96A TRP* 4.1 8.7 - - + -
210A GLY* 3.7 30.3 - - - +
215A GLN 3.7 16.3 - - - +
216A GLY* 4.2 0.7 - - - -
237A GLY 4.6 1.6 - - - +
238A PHE* 3.6 48.2 - - + -
279A SER* 2.9 23.0 + - - +
280A LEU* 3.0 8.0 + - + +
282A VAL* 1.3 80.0 - - - +
284A ARG* 1.3 53.3 + - - +
285A SER 3.2 0.2 - - - -
288A GLY* 4.2 5.6 - - - -
292A ARG* 2.5 34.5 + - - +
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLU* 4.0 9.7 + - - +
95A GLU* 2.6 38.0 + - - -
96A TRP* 3.5 36.5 - - + +
215A GLN* 2.7 52.8 + - - +
217A ARG* 4.1 7.1 - - - +
280A LEU* 2.8 46.7 + - + +
281A ALA* 3.8 5.6 - - - +
283A ILE* 1.3 75.7 - - - +
285A SER* 1.3 61.7 + - - +
289A ASP* 5.5 0.5 - - - +
292A ARG* 4.6 1.3 + - - -
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ALA 3.2 17.6 + - - -
282A VAL* 2.9 14.4 + - - -
284A ARG* 1.3 81.0 - - - +
286A ASP* 1.3 56.4 + - - +
287A GLU* 2.6 25.6 + - - +
288A GLY* 2.8 18.9 + - - -
289A ASP* 3.2 14.9 + - - +
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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
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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