Contacts of the helix formed by residues 273 - 290 (chain A) in PDB entry 3L49
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 GLN 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A SER* 4.9 0.2 + - - -
271A ALA 5.3 0.9 - - - +
272A GLN* 1.3 79.8 - - - +
274A PRO* 1.4 59.6 - - - +
275A SER* 3.3 3.1 - - - +
276A GLU* 3.0 28.2 + - + +
277A ILE* 2.9 33.5 + - - +
300A ALA* 4.6 2.0 - - + -
301A PRO* 3.2 56.1 + - - +
302A ALA* 4.9 1.4 - - - +
303A VAL* 5.5 6.5 - - - +
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Residues in contact with PRO 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 6.0 0.2 - - - +
45A TRP* 3.5 60.7 - - + +
48A LYS* 3.8 22.7 - - + +
49A ALA* 3.5 14.6 - - + +
250A ASP 5.1 1.1 - - - +
272A GLN 3.4 9.9 - - - +
273A GLN* 1.4 84.5 - - - +
275A SER* 1.3 57.4 + - - +
277A ILE* 3.3 9.8 + - + +
278A GLY 3.0 25.8 + - - -
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 3.4 28.1 + - - +
52A ALA* 3.3 18.9 - - - +
273A GLN* 3.3 1.0 - - - -
274A PRO* 1.3 79.2 - - - +
276A GLU* 1.3 59.9 + - - +
279A LYS* 3.3 22.7 + - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLN* 3.0 37.3 + - + +
275A SER* 1.3 78.0 - - - +
277A ILE* 1.3 59.2 + - - +
279A LYS* 3.3 21.3 + - - +
280A LEU* 2.9 58.9 + - - +
300A ALA* 4.3 7.9 - - + -
301A PRO* 5.7 1.5 - - + +
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Residues in contact with ILE 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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45A TRP* 4.0 24.5 - - + -
49A ALA* 5.2 0.7 - - + -
118A VAL* 3.9 31.9 - - + -
119A ASP* 4.8 0.7 - - - +
129A THR* 3.3 25.2 - - + +
130A THR* 3.6 23.6 - - - +
131A SER* 3.5 24.7 - - - +
272A GLN* 4.4 2.2 - - - +
273A GLN 2.9 26.2 + - - +
274A PRO* 3.6 7.2 - - + +
276A GLU* 1.3 75.0 - - - +
278A GLY* 1.3 62.9 + - - +
280A LEU* 3.3 2.2 + - - -
281A ALA* 3.0 21.3 + - - +
300A ALA* 3.7 11.0 - - + -
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.8 22.9 - - - -
52A ALA* 4.0 2.2 - - - -
53A GLN* 3.6 21.5 - - - +
118A VAL* 5.1 0.7 - - - -
274A PRO 3.0 13.3 + - - -
277A ILE* 1.3 80.0 - - - +
279A LYS* 1.3 60.9 + - - +
281A ALA* 3.5 2.6 + - - +
282A VAL* 3.4 26.3 + - - +
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Residues in contact with LYS 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 ALA* 4.0 5.2 - - + +
56A GLU* 3.4 50.9 + - + +
59A ARG* 4.4 12.4 - - - +
275A SER 3.3 15.3 + - - +
276A GLU* 3.3 27.1 + - - +
278A GLY* 1.3 75.4 - - - +
280A LEU* 1.3 61.7 + - + +
282A VAL 3.4 2.3 + - - -
283A GLN* 3.2 34.7 + - - +
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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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129A THR* 3.7 16.2 - - + -
276A GLU* 2.9 42.6 + - - +
277A ILE 3.3 0.2 + - - -
279A LYS* 1.3 76.0 - - + +
281A ALA* 1.3 60.7 + - - +
283A GLN* 3.3 20.2 + - + +
284A ASN* 3.0 30.3 + - - -
298A THR* 4.4 24.5 - - + -
299A PHE 4.4 2.0 - - - +
300A ALA* 4.2 23.6 - - + -
301A PRO* 5.9 0.9 - - + -
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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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53A GLN* 5.0 0.4 - - + -
92A ILE* 4.5 11.7 - - + -
116A PHE* 4.6 4.1 - - + -
117A THR 4.7 3.1 - - - +
118A VAL* 3.9 21.3 - - + -
127A ASN* 5.1 0.7 - - - +
129A THR* 3.4 21.9 + - - +
277A ILE 3.0 16.5 + - - +
278A GLY 3.7 6.5 - - - +
280A LEU* 1.3 77.4 - - - +
282A VAL* 1.3 57.2 + - - +
284A ASN* 3.3 6.5 + - - +
285A VAL* 3.1 29.5 + - - +
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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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29A LEU* 3.8 16.3 - - + +
34A ILE* 5.9 0.4 - - + -
53A GLN* 3.6 28.0 - - + +
56A GLU* 3.9 12.3 - - + -
57A ILE* 3.7 31.2 - - + +
60A LEU* 4.1 2.7 - - + -
92A ILE* 3.8 17.9 - - + -
278A GLY 3.4 14.7 + - - +
279A LYS 3.8 7.2 - - - +
280A LEU 3.3 0.6 - - - -
281A ALA* 1.3 75.7 - - - +
283A GLN* 1.3 57.0 + - - +
285A VAL* 3.2 10.5 + - + +
286A ALA* 2.8 25.1 + - - +
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Residues in contact with GLN 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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56A GLU* 2.9 33.1 + - - +
59A ARG* 4.2 7.3 - - - +
60A LEU* 4.5 7.7 - - + +
279A LYS* 3.2 24.6 + - - +
280A LEU* 3.6 22.7 - - + +
281A ALA 3.3 0.2 - - - -
282A VAL* 1.3 75.3 - - - +
284A ASN* 1.3 61.3 + - - +
286A ALA* 3.7 10.2 - - + +
287A ARG* 2.9 30.0 + - - +
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Residues in contact with ASN 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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116A PHE* 3.5 7.4 - - + -
127A ASN* 2.9 25.1 + - - +
129A THR* 2.9 27.1 + - - -
280A LEU 3.0 14.6 + - - -
281A ALA 3.3 8.0 + - - +
283A GLN* 1.3 75.5 - - - +
285A VAL* 1.3 64.3 + - - +
287A ARG* 4.3 7.5 - - - -
288A HIS* 3.1 25.5 + - - +
294A VAL* 3.4 21.9 - - + +
295A LYS 5.1 0.9 + - - -
298A THR* 2.9 22.2 + - - +
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.8 1.6 - - + -
34A ILE* 3.7 33.0 - - + -
90A ALA* 3.8 16.2 - - + -
92A ILE* 3.9 24.7 - - + -
116A PHE* 3.5 31.4 - - + -
281A ALA 3.1 16.1 + - - +
282A VAL* 3.2 9.2 + - + +
284A ASN* 1.3 74.9 - - - +
286A ALA* 1.3 62.9 + - - +
288A HIS* 3.2 3.1 + - - +
289A LEU* 3.1 30.5 + - + +
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Residues in contact with ALA 286 (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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28A SER* 4.2 17.3 + - - +
29A LEU* 3.8 25.8 - - + -
60A LEU* 3.9 18.4 - - + -
282A VAL 2.8 19.5 + - - +
283A GLN* 4.0 7.6 - - + +
285A VAL* 1.3 73.8 - - - +
287A ARG* 1.3 61.4 + - - +
289A LEU* 3.8 2.1 + - - +
290A ALA* 3.4 22.2 + - - +
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Residues in contact with ARG 287 (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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283A GLN 2.9 20.6 + - - +
284A ASN* 3.7 9.9 - - - +
285A VAL 3.2 0.2 - - - -
286A ALA* 1.3 75.8 - - - +
288A HIS* 1.3 65.2 + - - +
290A ALA* 3.2 10.1 + - - +
292A GLN* 3.1 65.9 + - + +
293A GLU* 2.8 37.4 + - - +
294A VAL* 3.7 9.9 - - + +
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Residues in contact with HIS 288 (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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114A PRO* 4.0 19.9 - - + +
116A PHE* 3.5 22.7 - + + -
126A ILE* 3.6 32.7 - - + +
284A ASN 3.1 15.7 + - - +
285A VAL 3.6 1.3 - - - +
287A ARG* 1.3 79.5 - - - +
289A LEU* 1.3 69.9 + - + +
291A GLY* 3.1 18.5 + - - -
292A GLN 3.9 8.4 + - - +
294A VAL* 3.6 12.5 - - + +
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Residues in contact with LEU 289 (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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28A SER 5.8 1.3 - - - +
29A LEU* 4.3 11.9 - - + -
32A LYS* 4.5 27.9 + - + +
34A ILE* 4.0 15.9 - - + -
89A ASP* 3.7 32.8 - - + +
90A ALA* 5.0 0.7 - - + -
114A PRO* 4.6 4.5 - - + -
285A VAL* 3.1 37.5 + - + +
286A ALA* 4.3 4.0 - - - +
288A HIS* 1.3 87.8 - - + +
290A ALA* 1.3 56.7 + - - +
291A GLY 3.1 7.7 + - - -
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Residues in contact with ALA 290 (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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28A SER 5.8 2.0 - - - +
286A ALA 3.4 15.7 + - - +
287A ARG* 3.2 7.4 + - - +
289A LEU* 1.3 76.1 - - - +
291A GLY* 1.3 60.8 + - - +
292A GLN* 3.4 24.8 + - - +
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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