Contacts of the helix formed by residues 285 - 305 (chain B) in PDB entry 3DDN
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 THR 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ARG* 4.2 6.7 - - - -
136A SER* 4.6 2.4 + - - -
137A GLY* 3.2 26.1 + - - +
138A THR 3.6 3.5 + - - -
139A GLU* 3.6 10.2 + - + +
102B SER* 2.7 32.5 + - - +
283B ALA 3.1 4.6 + - - -
284B SER* 1.3 73.9 + - - +
286B ALA* 1.3 63.4 + - - +
287B GLU* 3.3 11.9 - - - +
288B ALA* 2.8 27.4 - - + +
289B GLN* 3.1 23.5 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 4.2 9.1 + - - +
137A GLY 3.8 6.5 + - - +
14B ALA* 5.3 0.9 - - - +
285B THR* 1.3 71.8 - - - +
287B GLU* 1.3 69.8 + - + +
289B GLN* 3.6 5.7 + - - +
290B ASP* 2.9 30.1 + - - +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLY 4.2 0.4 - - - +
138A THR* 3.9 8.1 - - - +
139A GLU* 3.0 49.8 + - + +
141A PHE 6.1 0.7 - - - +
143A LYS* 2.9 35.9 + - - +
252A ARG* 5.3 3.1 + - - -
285B THR* 3.5 5.5 + - - +
286B ALA* 1.3 87.8 + - - +
288B ALA* 1.3 60.0 + - - +
290B ASP* 3.6 7.9 - - - +
291B ARG* 3.1 27.4 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 4.0 2.4 + - - +
98B SER* 3.5 27.6 - - - +
99B ASN 4.9 0.2 - - - +
102B SER* 3.8 12.3 - - - +
283B ALA* 3.6 22.0 - - + +
285B THR* 2.8 21.8 - - + +
287B GLU* 1.3 73.0 - - - +
289B GLN* 1.3 57.8 + - - +
291B ARG* 3.3 2.4 + - - +
292B ALA* 2.7 36.2 + - - +
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS 4.8 1.7 - - - +
13B LEU* 5.0 0.3 - - - -
14B ALA* 3.4 24.9 + - + +
51B ARG* 3.0 45.2 + - - +
73B ALA* 3.5 20.1 + - - +
74B GLY* 5.2 0.6 - - - -
283B ALA* 4.6 8.6 + - - +
284B SER* 5.7 0.4 - - - -
285B THR 3.1 20.5 + - - +
286B ALA* 3.9 6.1 - - - +
288B ALA* 1.3 74.9 - - - +
290B ASP* 1.3 60.6 + - - +
292B ALA* 3.2 6.3 + - - +
293B GLY* 2.8 26.5 + - - -
600B HPV 2.6 27.6 + - - -
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Residues in contact with ASP 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 3.7 7.1 - - + +
15B PRO* 5.9 0.7 - - + +
16B SER* 2.9 44.9 + - - -
286B ALA 2.9 20.3 + - - +
287B GLU* 3.6 8.8 - - - +
289B GLN* 1.3 78.0 - - - +
291B ARG* 1.3 65.4 + - - +
294B THR* 3.1 17.7 + - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 4.7 12.4 + - - +
98B SER* 4.0 17.0 - - - +
287B GLU 3.1 17.4 + - - +
288B ALA* 3.7 3.8 - - - +
290B ASP* 1.3 78.5 + - - +
292B ALA* 1.3 60.1 + - - +
294B THR* 3.2 13.0 + - - -
295B ASP* 2.9 58.8 + - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 3.7 33.4 - - + +
74B GLY* 4.6 0.2 - - - -
95B ALA* 3.8 5.2 - - + -
98B SER* 3.6 20.5 - - - +
288B ALA 2.7 21.8 + - - +
289B GLN* 3.6 11.9 - - - +
291B ARG* 1.3 72.4 - - - +
293B GLY* 1.3 61.9 + - - +
295B ASP* 3.6 0.5 - - - +
296B VAL* 3.1 30.5 + - - +
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Residues in contact with GLY 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 5.6 0.2 - - - -
14B ALA* 4.8 0.7 - - - -
16B SER* 4.2 1.1 - - - -
17B THR* 3.1 32.1 - - - +
73B ALA* 4.7 4.7 - - - +
289B GLN 2.8 19.7 + - - -
290B ASP 3.7 1.8 - - - -
292B ALA* 1.3 72.8 - - - +
294B THR* 1.3 63.5 + - - +
295B ASP 3.4 0.2 + - - -
296B VAL* 3.4 8.7 - - - +
297B ALA* 3.1 22.9 + - - +
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Residues in contact with THR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER* 3.5 32.8 - - - +
20B ALA* 4.5 11.0 - - + +
290B ASP* 3.1 11.8 + - - +
291B ARG* 3.2 23.2 + - - -
293B GLY* 1.3 75.1 - - - +
295B ASP* 1.3 64.9 + - - +
297B ALA* 3.5 7.3 + - - +
298B GLU* 3.1 23.0 + - - +
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASN 5.7 0.4 - - - -
95B ALA* 3.8 18.0 - - + +
96B PRO* 5.8 0.9 - - - -
97B THR* 4.8 4.3 + - - -
98B SER* 3.7 17.8 + - - -
291B ARG* 2.9 56.5 + - - +
292B ALA 3.6 4.9 - - - +
293B GLY 3.2 0.2 - - - -
294B THR* 1.3 73.9 + - - +
296B VAL* 1.3 64.5 + - - +
298B GLU* 3.2 8.1 + - - +
299B SER* 3.1 22.8 + - - -
311B ASP* 4.6 10.6 - - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.7 7.2 - - + -
17B THR* 4.4 3.1 - - + -
49B LEU* 3.8 23.1 - - + -
71B ALA* 3.8 18.4 - - + -
72B ARG 3.3 33.0 - - - +
73B ALA* 3.8 2.9 - - + +
93B VAL* 4.5 0.7 - - + -
94B ASN 4.5 6.1 - - - +
95B ALA* 4.3 7.6 - - + -
292B ALA 3.1 12.9 + - - +
293B GLY* 3.4 14.8 - - - +
295B ASP* 1.3 76.2 - - - +
297B ALA* 1.3 59.6 + - - +
299B SER* 3.6 7.3 - - - -
300B VAL* 2.9 33.8 + - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 4.0 7.4 - - + +
20B ALA* 3.8 27.6 - - + +
21B LEU* 3.6 30.9 - - + +
49B LEU* 5.4 0.2 - - - -
293B GLY 3.1 18.1 + - - +
294B THR 3.7 4.9 - - - +
295B ASP 3.2 0.2 - - - -
296B VAL* 1.3 79.5 - - - +
298B GLU* 1.3 62.3 + - - +
300B VAL* 3.4 2.9 + - - +
301B ARG* 3.0 24.1 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR 3.1 14.9 + - - +
295B ASP* 3.2 9.6 + - - +
297B ALA* 1.3 77.0 - - - +
299B SER* 1.3 61.3 + - - +
301B ARG* 2.9 48.5 + - - +
302B LEU* 3.1 44.1 + - + +
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.8 5.1 - - - +
93B VAL* 3.6 37.4 - - - +
295B ASP 3.1 12.5 + - - -
296B VAL 3.3 6.3 + - - -
298B GLU* 1.3 77.4 - - - +
300B VAL* 1.3 57.8 + - - +
302B LEU* 3.5 7.2 + - - +
303B ALA* 3.0 28.8 + - - +
309B VAL* 4.0 11.3 - - - +
310B PRO* 5.9 0.5 - - - +
311B ASP* 3.6 23.4 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.8 17.7 - - + -
21B LEU* 4.4 9.6 - - + -
25B VAL* 5.4 1.1 - - + -
47B ALA* 3.9 5.4 - - + -
49B LEU* 3.5 32.8 - - + -
69B ILE* 4.1 19.1 - - + -
71B ALA* 4.5 6.7 - - + -
296B VAL 2.9 20.3 + - - +
297B ALA 3.8 3.6 - - - +
299B SER* 1.3 72.3 - - - +
301B ARG* 1.3 67.8 + - - +
303B ALA* 3.1 2.6 + - - -
304B LEU* 2.8 48.1 + - + +
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 6.0 3.4 - - - +
21B LEU* 6.1 0.9 - - + -
25B VAL* 6.4 1.6 - - - -
297B ALA 3.0 14.4 + - - +
298B GLU* 2.9 46.5 + - - +
300B VAL* 1.3 77.1 - - - +
302B LEU* 1.3 79.1 + - - +
304B LEU* 3.2 5.6 + - - +
305B ALA* 2.8 36.7 + - + +
307B GLU* 4.7 11.5 + - - -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 3.1 38.3 + - + +
299B SER* 3.8 8.3 - - - +
301B ARG* 1.3 102.1 - - - +
303B ALA* 1.3 61.0 + - - +
305B ALA* 3.3 5.5 + - - -
306B GLY 3.2 3.3 + - - -
307B GLU* 2.8 56.9 + - + +
308B PHE 3.7 22.0 - - - +
309B VAL* 4.1 3.4 - - + -
310B PRO* 3.9 18.2 - - + -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LYS* 5.2 9.4 - - + +
69B ILE* 3.8 32.5 - - + -
91B LEU* 4.2 8.5 - - + -
299B SER 3.0 17.9 + - - +
300B VAL 3.1 4.0 + - - +
302B LEU* 1.3 75.4 - - - +
304B LEU* 1.3 65.5 + - + +
306B GLY* 3.3 12.0 + - - -
307B GLU 4.6 1.8 - - - -
309B VAL* 3.7 15.2 - - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 4.0 19.5 - - + -
7B VAL* 4.0 15.9 - - + -
25B VAL* 4.0 15.7 - - + -
46B ASP* 3.9 28.3 - - + +
47B ALA* 4.6 4.0 - - + -
68B LYS* 4.3 19.3 - - + +
69B ILE* 5.4 0.9 - - + -
300B VAL* 2.8 40.0 + - + +
301B ARG* 3.8 4.7 - - - +
303B ALA* 1.3 76.9 - - + +
305B ALA* 1.3 58.5 + - - +
306B GLY 3.0 8.1 + - - -
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ARG* 2.8 24.0 + - + +
302B LEU* 3.3 8.0 + - - +
304B LEU* 1.3 75.9 - - - +
306B GLY* 1.3 60.4 + - - -
307B GLU* 3.3 24.6 + - + +
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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
------------------------------------------------------------
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