Contacts of the helix formed by residues 285 - 305 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 2.9 27.5 + - - +
283A ALA 2.8 7.6 + - - -
284A SER* 1.3 76.0 + - - +
286A ALA* 1.3 63.5 + - - +
287A GLU* 3.2 21.3 - - + +
288A ALA 2.9 24.2 - - - +
289A GLN* 3.0 28.2 + - - +
116B ARG* 3.9 12.3 + - - -
136B SER* 4.7 1.1 - - - -
137B GLY* 3.5 22.5 + - - +
138B THR 4.0 0.2 - - - -
139B GLU* 3.8 6.5 + - + -
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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
----------------------------------------------------------
285A THR* 1.3 71.6 - - - +
287A GLU* 1.3 65.2 + - - +
289A GLN* 4.6 4.3 - - - +
290A ASP* 2.8 45.4 + - - +
136B SER* 4.1 11.1 + - - +
137B GLY 3.7 8.8 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A THR* 3.4 4.5 - - - +
286A ALA* 1.3 88.1 + - + +
288A ALA* 1.3 56.8 + - - +
290A ASP* 3.6 6.4 + - - +
291A ARG* 2.9 37.7 + - - +
137B GLY 4.0 0.7 - - - +
138B THR* 3.9 7.8 - - - +
139B GLU* 3.1 49.4 + - + +
141B PHE 6.0 0.7 - - - +
143B LYS* 2.5 41.3 + - - +
252B ARG* 5.1 2.8 + - - -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 3.8 23.1 + - - +
99A ASN* 4.3 7.4 - - + -
102A SER* 3.6 14.6 - - - +
283A ALA* 3.6 23.6 - - + +
285A THR* 2.9 17.3 - - + +
287A GLU* 1.3 73.2 - - - +
289A GLN* 1.3 66.2 + - - +
291A ARG* 3.9 1.3 - - - +
292A ALA* 3.0 28.8 + - - +
139B GLU* 4.1 2.0 + - - -
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 4.7 1.4 - - - +
51A ARG* 3.4 43.6 + - - +
73A ALA* 4.5 10.2 + - - +
99A ASN* 6.1 0.2 - - - +
283A ALA* 3.3 30.8 + - - +
284A SER* 5.5 1.1 - - - -
285A THR 3.0 19.3 + - - +
286A ALA* 4.0 4.5 - - - +
288A ALA* 1.3 77.0 + - - +
290A ASP* 1.3 70.3 + - - +
292A ALA* 3.4 9.1 + - - +
293A GLY* 3.2 17.3 + - - -
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.6 22.3 + - + +
286A ALA* 2.8 33.7 + - - +
287A GLU* 3.8 6.1 - - - +
289A GLN* 1.3 74.6 - - - +
291A ARG* 1.3 56.4 + - - +
293A GLY* 3.1 3.8 + - - -
294A THR* 2.9 35.2 + - + +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR 4.9 2.5 + - - -
98A SER* 3.6 24.1 + - - +
101A HIS* 4.0 23.6 - - - +
287A GLU* 2.9 27.1 + - - +
288A ALA 3.5 4.0 + - - +
289A GLN 3.2 0.2 - - - -
290A ASP* 1.3 72.9 - - - +
292A ALA* 1.3 57.7 + - - +
294A THR* 3.9 8.3 - - - +
295A ASP* 2.7 56.5 + - - +
139B GLU* 2.6 43.6 + - - -
141B PHE* 5.1 6.4 - - - -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 3.6 31.9 - - + +
74A GLY* 3.8 2.7 - - - +
95A ALA* 3.5 7.7 - - - +
98A SER* 3.4 21.9 - - - +
288A ALA 3.0 18.7 + - - +
289A GLN* 3.5 12.3 - - - +
291A ARG* 1.3 75.1 - - - +
293A GLY* 1.3 57.1 + - - +
296A VAL* 3.1 29.6 + - - +
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Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.3 8.5 - - - -
17A THR* 3.6 20.1 - - - +
18A VAL* 4.8 1.9 - - - +
73A ALA* 4.1 12.5 - - - +
289A GLN 3.2 4.9 + - - -
290A ASP 3.1 7.2 + - - -
291A ARG 3.1 0.6 - - - -
292A ALA* 1.3 76.6 - - - +
294A THR* 1.3 59.0 + - - +
295A ASP 3.2 1.1 - - - -
296A VAL* 3.5 3.2 + - - +
297A ALA* 2.8 30.0 + - - +
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER 5.1 1.3 - - - +
17A THR* 3.1 27.1 - - + +
20A ALA* 4.4 7.8 - - - +
290A ASP* 2.9 18.9 + - + +
291A ARG* 3.5 13.2 + - - +
293A GLY* 1.3 72.0 - - - +
295A ASP* 1.3 71.7 + - - +
297A ALA* 3.4 4.3 + - - +
298A GLU* 3.2 19.2 + - - +
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA* 3.6 20.6 - - + +
96A PRO* 5.3 0.9 - - - +
97A THR* 4.2 8.9 + - - -
98A SER* 3.4 28.6 + - - -
291A ARG* 2.7 32.5 + - - +
294A THR* 1.3 79.3 + - - +
296A VAL* 1.3 59.0 + - - +
298A GLU* 2.8 24.9 + - - +
299A SER* 3.0 14.8 + - - -
311A ASP* 5.1 8.6 - - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.7 0.9 - - + -
49A LEU* 4.2 18.8 - - + -
71A ALA* 3.8 25.8 - - + -
72A ARG 3.2 29.2 - - - +
73A ALA* 4.3 14.1 - - + +
93A VAL* 3.8 13.0 - - + -
94A ASN 3.8 11.4 + - - +
292A ALA 3.1 13.7 + - - +
293A GLY* 3.8 7.9 - - - +
295A ASP* 1.3 79.3 - - - +
297A ALA* 1.3 63.4 + - - +
299A SER* 3.8 7.0 - - - -
300A VAL* 3.0 30.0 + - - +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.5 38.6 - - + +
20A ALA* 3.9 14.6 - - + -
21A LEU* 3.3 19.9 + - + +
49A LEU* 5.0 0.4 - - - -
293A GLY 2.8 22.5 + - - +
294A THR* 3.7 6.5 - - - +
295A ASP 3.1 0.2 - - - -
296A VAL* 1.3 74.3 - - - +
298A GLU* 1.3 57.1 + - - +
300A VAL* 4.6 0.9 - - - -
301A ARG* 3.1 22.2 + - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 4.0 15.3 - - + +
294A THR 3.2 10.8 + - - +
295A ASP* 2.8 11.2 + - - +
297A ALA* 1.3 75.7 - - - +
299A SER* 1.3 65.9 + - - +
301A ARG* 2.9 47.0 + - - +
302A LEU* 2.9 41.3 + - + +
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 5.8 0.9 - - - -
93A VAL* 3.7 29.9 - - - +
94A ASN 4.5 1.2 + - - -
295A ASP 3.0 10.9 + - - -
296A VAL* 3.8 9.8 - - - -
298A GLU* 1.3 76.3 - - - +
300A VAL* 1.3 58.5 + - - +
302A LEU* 3.5 11.2 + - - +
303A ALA* 3.0 29.3 + - - +
309A VAL* 4.0 9.5 - - - +
310A PRO* 5.8 0.9 - - - +
311A ASP* 3.4 29.6 + - - +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.4 3.4 - - + -
21A LEU* 3.7 19.3 - - + -
47A ALA* 3.9 22.2 - - + -
49A LEU* 3.5 26.0 - - + -
69A ILE* 4.1 21.3 - - + -
71A ALA* 3.7 14.6 - - + -
296A VAL 3.0 22.1 + - - +
297A ALA* 3.9 4.7 - - - +
298A GLU 3.1 0.2 - - - -
299A SER* 1.3 73.9 - - - +
301A ARG* 1.3 65.8 + - - +
303A ALA* 3.9 0.9 - - - +
304A LEU* 3.1 31.9 + - + +
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 3.2 24.5 - - - +
21A LEU* 4.4 4.9 - - - +
22A GLY* 4.5 13.9 - - - +
297A ALA 3.1 14.1 + - - +
298A GLU* 2.9 40.4 + - - +
300A VAL* 1.3 75.8 - - - +
302A LEU* 1.3 89.1 + - - +
304A LEU* 3.0 7.2 + - - +
305A ALA* 2.9 35.6 + - + +
307A GLU* 5.0 5.1 + - - -
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Residues in contact with LEU 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 GLU* 2.9 35.5 + - + +
299A SER* 3.8 7.6 - - - +
301A ARG* 1.3 106.1 - - - +
303A ALA* 1.3 60.3 + - - +
305A ALA* 3.1 7.6 + - - -
307A GLU* 2.9 58.2 + - + +
308A PHE 3.9 22.7 - - - +
309A VAL* 4.3 3.1 - - + -
310A PRO* 4.0 17.7 - - + -
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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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68A LYS* 6.1 1.4 - - - +
69A ILE* 3.1 31.0 - - + +
91A LEU* 3.9 13.2 - - + -
299A SER 3.0 17.3 + - - +
301A ARG 3.2 0.2 - - - -
302A LEU* 1.3 77.4 - - - +
304A LEU* 1.3 59.2 + - - +
306A GLY* 3.6 9.5 + - - -
307A GLU 4.4 2.6 - - - +
309A VAL* 3.6 19.5 - - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.4 16.6 - - + -
7A VAL* 4.1 16.4 - - + -
21A LEU* 5.8 0.7 - - + -
25A VAL* 3.9 28.5 - - + -
46A ASP* 4.6 12.1 - - + +
47A ALA* 4.8 2.0 - - + -
68A LYS* 4.4 24.0 - - + -
69A ILE* 4.1 19.3 - - + -
300A VAL* 3.1 25.1 + - + +
301A ARG* 3.0 7.1 + - - +
303A ALA* 1.3 74.0 - - - +
305A ALA* 1.3 57.1 + - - +
306A GLY 3.1 8.3 + - - -
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 2.9 26.5 + - + +
302A LEU* 3.1 7.8 + - - +
304A LEU* 1.3 77.0 - - - +
306A GLY* 1.3 55.3 + - - -
307A GLU* 2.8 27.4 + - + +
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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