Contacts of the helix formed by residues 289 - 306 (chain A) in PDB entry 1DG3
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 ASN 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.1 25.2 + - - +
36A GLN 3.2 23.6 - - - +
37A PRO* 4.2 1.8 - - + -
38A MET* 3.6 7.2 - - - -
287A GLN 3.5 3.9 + - - +
288A VAL* 1.3 76.9 - - - +
290A GLY* 1.3 60.5 + - - +
291A PRO* 3.3 15.6 - - - +
292A ARG* 3.2 33.6 + - - +
293A LEU* 2.9 26.0 + - - +
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Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 2.9 26.3 - - - +
34A ILE 2.8 17.6 + - - -
36A GLN 4.0 0.2 + - - -
38A MET* 3.4 22.1 - - - +
289A ASN* 1.3 70.3 - - - +
291A PRO* 1.3 57.9 - - - +
293A LEU* 3.1 3.3 + - - +
294A GLU* 2.8 28.9 + - - +
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Residues in contact with PRO 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU 3.4 2.7 - - - +
32A SER* 3.5 22.2 - - - +
34A ILE 3.3 11.9 - - - +
35A THR* 5.4 4.3 - - + -
289A ASN* 3.3 19.5 - - - +
290A GLY* 1.3 90.2 - - - +
292A ARG* 1.3 56.9 + - + +
294A GLU* 3.5 16.3 + - - +
295A SER* 3.0 26.7 + - - -
319A LEU* 4.7 1.9 - - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 5.5 0.4 - - + -
286A ILE* 3.1 25.5 - - - +
287A GLN* 2.8 41.1 + - - +
288A VAL* 4.1 11.0 - - + +
289A ASN* 3.2 27.6 + - - +
290A GLY 3.2 0.8 - - - -
291A PRO* 1.3 77.2 - - + +
293A LEU* 1.3 65.6 + - - +
295A SER* 3.2 4.2 + - - -
296A LEU* 3.0 26.1 + - - +
319A LEU* 3.5 26.2 - - + +
323A GLU* 2.7 44.1 + - - +
373A PHE* 4.2 8.1 - - - -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.2 6.7 - - + -
31A LEU* 4.1 24.5 - - + -
38A MET* 4.0 19.3 - - - -
40A VAL* 4.8 8.3 - - + -
94A VAL* 4.4 17.3 - - + -
96A LEU* 5.5 2.5 - - + -
122A LEU* 4.0 39.9 - - + +
280A LYS* 5.9 0.2 - - + -
288A VAL* 3.7 13.6 - - + +
289A ASN 2.9 16.9 + - - +
290A GLY* 3.6 3.6 - - - +
292A ARG* 1.3 72.5 - - - +
294A GLU* 1.3 67.4 + - - +
296A LEU* 3.2 12.0 + - + +
297A VAL* 2.9 31.8 + - + +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.6 41.7 - - + +
29A LYS* 5.2 2.4 - - - +
31A LEU* 4.1 19.9 - - + +
32A SER* 3.1 24.8 - - - -
290A GLY 2.8 16.1 + - - +
291A PRO* 3.5 10.5 - - + +
293A LEU* 1.3 76.4 - - - +
295A SER* 1.3 63.3 + - - +
297A VAL* 3.3 2.5 + - - +
298A LEU* 3.0 36.2 + - + +
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO 3.0 13.8 + - - -
292A ARG 3.4 9.9 - - - -
294A GLU* 1.3 78.4 - - - +
296A LEU* 1.3 58.8 + - - +
298A LEU* 3.3 8.7 + - - +
299A THR* 2.9 38.7 + - - -
315A ALA 4.9 2.3 + - - -
318A ALA* 4.8 2.1 - - - +
319A LEU* 3.8 34.4 + - - +
322A ILE* 4.5 12.6 - - - +
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Residues in contact with LEU 296 (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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121A LEU 5.0 1.6 - - - +
122A LEU* 4.0 14.8 - - + -
280A LYS* 4.9 9.6 - - - -
282A LEU* 4.0 37.5 - - + -
288A VAL* 4.4 13.7 - - + -
292A ARG 3.0 18.3 + - - +
293A LEU* 3.2 20.8 + - + +
295A SER* 1.3 76.1 - - - +
297A VAL* 1.3 63.8 + - - +
299A THR* 3.8 4.2 - - - -
300A TYR* 2.9 46.0 + - + +
315A ALA* 3.6 30.1 - - + +
319A LEU* 5.9 2.5 - - + -
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.1 26.7 - - + -
14A ILE* 3.9 28.0 - - + -
23A ALA* 4.1 19.1 - - + -
28A LEU* 4.2 12.1 - - + -
31A LEU* 4.8 0.4 - - + -
118A LEU* 6.3 0.4 - - - -
122A LEU* 4.1 24.2 - - + -
293A LEU* 2.9 25.0 + - + +
294A GLU* 3.6 7.6 - - - +
295A SER 3.3 0.2 - - - -
296A LEU* 1.3 75.7 - - - +
298A LEU* 1.3 57.7 + - - +
300A TYR* 4.1 1.3 - - - +
301A VAL* 2.9 36.8 + - + +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.3 11.9 - - + -
28A LEU* 3.5 28.7 - - + -
294A GLU* 3.0 38.7 + - + +
295A SER* 3.7 6.7 - - - +
297A VAL* 1.3 77.3 - - - +
299A THR* 1.3 57.4 + - - +
301A VAL* 4.8 3.1 - - - -
302A ASN* 2.8 51.9 + - - +
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER* 2.9 22.2 + - - -
296A LEU 3.8 3.1 - - - -
298A LEU* 1.3 76.9 - - - +
300A TYR* 1.3 64.4 + - + +
302A ASN* 3.9 5.1 - - - +
303A ALA* 3.0 29.5 + - + +
311A CYS 4.9 2.7 - - - +
314A ASN* 4.6 6.7 - - + +
315A ALA* 3.8 35.1 - - + +
318A ALA* 3.9 20.4 - - + +
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Residues in contact with TYR 300 (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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118A LEU* 3.7 19.5 - - + -
121A LEU* 3.8 41.4 + - + +
122A LEU* 4.0 14.6 - - + -
282A LEU* 5.2 3.1 - - - +
296A LEU* 2.9 43.0 + - + +
297A VAL* 4.1 2.0 - - - +
299A THR* 1.3 78.1 - - + +
301A VAL* 1.3 65.9 + - - +
303A ALA* 3.4 3.4 + - - +
304A ILE* 3.2 29.7 + - - +
310A PRO* 3.6 21.2 - - + +
311A CYS 3.7 19.1 - - - -
312A MET* 3.5 24.7 - - - +
315A ALA* 3.6 25.2 - - + +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.7 38.8 - - + -
21A LEU* 3.6 32.8 - - + +
23A ALA* 4.5 14.4 - - + +
118A LEU* 4.8 8.1 - - + -
297A VAL* 2.9 25.3 + - + +
298A LEU* 4.2 3.1 - - + +
300A TYR* 1.3 73.9 - - - +
302A ASN* 1.3 65.2 + - - +
304A ILE* 3.3 7.4 + - - +
305A SER* 2.9 37.3 + - - +
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Residues in contact with ASN 302 (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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298A LEU* 2.8 44.5 + - - +
299A THR* 3.9 4.8 - - - +
301A VAL* 1.3 81.4 - - - +
303A ALA* 1.3 60.0 + - - +
305A SER* 3.4 7.0 + - - -
306A SER* 2.7 35.7 + - - +
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Residues in contact with ALA 303 (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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299A THR* 3.0 20.3 + - + +
300A TYR* 3.5 6.5 - - - +
302A ASN* 1.3 76.9 - - - +
304A ILE* 1.3 60.6 + - - +
306A SER* 3.1 9.8 + - - -
308A ASP* 2.9 36.7 + - + +
309A LEU 3.9 21.5 - - - +
310A PRO* 4.0 9.6 - - + -
311A CYS 5.2 0.7 - - - +
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Residues in contact with ILE 304 (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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21A LEU* 3.9 24.2 - - + -
114A TRP* 3.5 56.8 - - + +
118A LEU* 4.0 20.2 - - + -
300A TYR 3.2 16.4 + - - +
301A VAL* 3.7 6.3 - - - +
303A ALA* 1.3 71.2 - - - +
305A SER* 1.3 59.8 + - - +
306A SER 3.0 9.4 + - - -
307A GLY* 3.0 14.0 + - - -
308A ASP 3.7 6.7 - - - +
310A PRO* 3.5 24.2 - - + -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.8 25.6 + - - +
301A VAL* 2.9 21.5 + - - +
302A ASN* 3.7 7.6 - - - -
304A ILE* 1.3 75.5 - - - +
306A SER* 1.3 58.9 + - - +
307A GLY 3.4 0.8 + - - -
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Residues in contact with SER 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASN* 2.7 23.2 + - - +
303A ALA* 3.5 6.3 - - - -
304A ILE 3.0 1.6 - - - -
305A SER* 1.3 78.4 - - - +
307A GLY* 1.3 62.3 + - - +
308A ASP* 3.3 18.6 + - - +
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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