Contacts of the helix formed by residues 319 - 335 (chain B) in PDB entry 2D2I
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 GLU 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG* 2.8 53.0 + - - +
13B ILE* 4.3 8.4 - - + +
16B ASN* 3.7 16.8 + - - +
52B VAL* 4.1 7.2 - - - +
53B LEU* 5.5 1.2 - - - +
240B PRO 4.7 5.8 - - - +
241B ASN* 3.5 28.8 - - - +
317B ASP* 3.0 4.7 + - - +
318B ASN* 1.3 80.7 - - - +
320B TRP* 1.3 61.7 + - + +
322B TYR* 3.6 1.4 + - - +
323B SER* 2.9 35.2 + - - -
2341B NAP 3.6 21.3 + - - +
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Residues in contact with TRP 320 (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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16B ASN* 3.5 23.8 - - - +
19B ARG* 4.0 26.7 - - + -
20B CYS* 3.7 37.2 - - - -
23B GLY* 6.3 0.9 - - - -
53B LEU* 3.5 26.2 - - + -
290B GLY* 3.5 32.9 + - - -
291B THR 3.6 8.3 - - - -
292B ASP* 2.7 21.9 + - - -
317B ASP* 2.9 26.0 + - - +
319B GLU* 1.3 72.6 - - - +
321B GLY* 1.3 65.0 + - - +
323B SER* 3.2 3.6 + - - -
324B GLN* 3.0 36.8 + - + +
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Residues in contact with GLY 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B THR 3.7 16.8 - - - -
292B ASP 3.9 10.1 - - - -
293B GLU 4.2 8.1 - - - -
294B SER* 5.4 3.1 - - - -
316B TYR* 6.4 0.2 - - - -
317B ASP* 2.9 19.6 + - - +
320B TRP* 1.3 77.6 - - - +
322B TYR* 1.3 62.0 + - - +
324B GLN* 3.2 10.9 + - - +
325B ARG* 3.3 20.6 + - - +
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Residues in contact with TYR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.3 11.2 - - + -
122B THR* 2.9 35.0 - - - -
123B ALA 3.2 0.5 + - - -
152B ASN* 3.1 32.4 - - - +
153B ALA 2.6 28.4 + - - -
154B SER 3.8 10.1 - - - -
155B CYS* 3.7 19.7 - - + -
158B ASN* 3.9 9.4 - - + -
317B ASP 3.6 4.4 + - - +
318B ASN 3.2 20.6 - - - +
319B GLU 3.6 0.6 + - - +
321B GLY* 1.3 77.0 - - - +
323B SER* 1.3 58.9 + - - +
325B ARG* 2.9 23.1 + - - +
326B VAL* 3.0 29.8 + - + +
2341B NAP 3.3 28.3 - + - -
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 3.8 16.8 + - - +
16B ASN* 3.1 30.4 - - - +
17B PHE* 3.7 14.5 + - - -
20B CYS* 3.9 7.0 - - - -
319B GLU 2.9 20.9 + - - -
320B TRP 3.2 4.2 + - - -
322B TYR* 1.3 76.7 - - - +
324B GLN* 1.3 60.7 + - - +
326B VAL* 3.3 12.2 + - - +
327B VAL* 3.1 26.7 + - - +
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B CYS* 3.1 32.2 - - - +
24B ARG* 3.1 44.9 + - - +
292B ASP* 3.0 37.7 - - + +
320B TRP* 3.0 28.0 + - + +
321B GLY 3.4 9.2 - - - +
323B SER* 1.3 76.3 - - - +
325B ARG* 1.3 76.0 + - - +
327B VAL* 3.3 0.7 + - - +
328B ASP* 2.9 23.9 + - - -
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Residues in contact with ARG 325 (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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24B ARG* 5.5 0.4 - - - +
135B ILE* 3.8 24.7 - - + +
152B ASN* 3.6 16.9 - - - +
158B ASN* 3.4 16.6 - - - +
274B GLY 4.0 14.0 + - - -
275B ILE* 4.1 8.4 - - - +
292B ASP* 2.9 33.7 + - - +
293B GLU* 3.6 1.6 - - - +
294B SER* 2.7 47.6 + - - +
321B GLY 3.3 8.5 + - - +
322B TYR* 2.9 10.6 + - - +
324B GLN* 1.3 90.9 - - - +
326B VAL* 1.3 60.4 + - - +
327B VAL 3.1 1.8 - - - -
328B ASP* 2.8 30.1 + - - +
329B LEU* 2.8 29.6 + - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.9 1.6 - - + -
17B PHE* 3.2 30.7 - - + -
96B ILE* 4.5 7.2 - - + -
120B LEU* 4.1 6.4 - - + +
122B THR* 4.2 22.4 - - + -
152B ASN* 3.6 23.8 - - + +
322B TYR* 3.0 35.0 - - + +
323B SER* 3.3 10.7 + - - +
325B ARG* 1.3 73.2 - - - +
327B VAL* 1.3 66.3 + - - +
329B LEU* 3.8 2.9 - - - +
330B ALA* 2.9 24.1 + - - +
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 3.4 32.8 - - + +
20B CYS* 3.9 21.3 - - + -
21B TRP* 4.0 17.0 - - + +
24B ARG* 3.1 33.4 - - + +
29B LEU* 4.8 2.0 - - + -
323B SER 3.1 18.9 + - - +
324B GLN 3.5 2.2 - - - +
326B VAL* 1.3 78.9 - - - +
328B ASP* 1.3 62.6 + - - +
330B ALA* 3.2 2.1 + - - +
331B GLU* 2.9 44.7 + - + +
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 2.7 30.2 + - - +
135B ILE* 3.8 23.7 - - + +
275B ILE* 5.0 1.4 - - - +
324B GLN 2.9 14.3 + - - -
325B ARG* 2.8 41.5 + - - +
327B VAL* 1.3 77.6 - - - +
329B LEU* 1.3 57.1 + - - +
331B GLU* 3.3 7.6 + - - +
332B LEU* 2.8 27.0 + - - +
335B ARG* 5.6 0.7 + - - -
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.8 20.3 - - + +
133B TYR* 4.0 29.6 - - + +
135B ILE* 3.9 15.2 - - + +
142B TYR* 4.7 4.0 - - + -
150B ILE* 4.1 12.8 - - + -
151B SER 4.0 7.6 - - - +
152B ASN* 3.4 39.7 - - + +
325B ARG 2.8 18.7 + - - +
326B VAL* 3.9 4.0 - - - +
328B ASP* 1.3 71.7 - - - +
330B ALA* 1.3 61.1 + - - +
332B LEU* 3.2 15.0 + - + -
333B ALA* 2.9 26.3 + - - +
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Residues in contact with ALA 330 (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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3B ILE* 4.0 2.6 - - - +
5B VAL* 5.7 0.2 - - + -
17B PHE* 4.5 1.1 - - + -
29B LEU* 3.6 23.6 - - + +
94B LEU* 3.8 24.7 - - + -
96B ILE* 4.2 8.7 - - + -
120B LEU* 4.0 8.7 - - + +
326B VAL 2.9 19.1 + - - +
327B VAL* 3.6 5.4 - - - +
329B LEU* 1.3 75.9 - - - +
331B GLU* 1.3 57.6 + - - +
333B ALA* 3.3 4.3 + - - +
334B ALA* 2.9 26.3 + - - +
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Residues in contact with GLU 331 (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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21B TRP* 4.3 1.2 - - - -
24B ARG* 5.2 6.7 + - - +
26B ASN 4.3 3.1 - - - +
27B THR* 2.4 34.4 + - - -
28B ASP* 3.0 30.4 + - - +
29B LEU* 3.6 12.9 - - + +
327B VAL* 2.9 38.1 + - + +
328B ASP* 3.4 11.2 - - - +
330B ALA* 1.3 75.2 - - - +
332B LEU* 1.3 64.1 + - - +
334B ALA* 3.2 4.9 + - - +
335B ARG* 3.0 36.0 + - - +
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Residues in contact with LEU 332 (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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133B TYR* 5.8 0.2 - - + -
135B ILE* 4.7 4.3 - - + -
139B ASP* 3.8 28.9 - - + +
142B TYR* 3.6 29.8 - - + -
328B ASP 2.8 14.3 + - - +
329B LEU* 3.5 23.6 - - + +
331B GLU* 1.3 72.7 - - - +
333B ALA* 1.3 67.7 + - - +
335B ARG* 3.3 30.0 + - - +
336B LYS* 2.9 47.7 - - + +
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Residues in contact with ALA 333 (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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3B ILE* 4.8 2.7 - - + -
94B LEU* 4.8 10.3 - - + -
118B LYS* 4.9 6.5 - - + -
142B TYR* 3.6 32.4 + - + +
144B HIS* 4.9 2.3 - - + -
150B ILE* 4.9 7.6 - - + -
329B LEU 2.9 13.6 + - - +
330B ALA* 3.5 11.2 - - - +
331B GLU 3.2 0.2 - - - -
332B LEU* 1.3 79.0 - - - +
334B ALA* 1.3 61.2 + - - +
336B LYS* 3.0 22.5 + - - +
337B SER* 3.4 5.4 + - - -
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.7 9.4 + - - +
3B ILE* 3.7 38.3 - - + +
28B ASP* 3.7 26.7 - - + +
29B LEU* 3.9 4.9 - - + -
330B ALA 2.9 14.8 + - - +
331B GLU 3.4 9.4 - - - +
332B LEU 3.1 0.2 - - - -
333B ALA* 1.3 72.9 - - - +
335B ARG* 1.3 52.8 + - - +
336B LYS 2.8 16.1 + - - -
337B SER* 3.7 6.4 + - - -
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Residues in contact with ARG 335 (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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1B MET 5.5 3.6 - - - +
28B ASP* 3.4 24.2 - - - +
328B ASP 5.6 0.4 + - - -
331B GLU* 3.0 22.5 + - - +
332B LEU* 3.3 35.0 + - - +
334B ALA* 1.3 73.3 - - - +
336B LYS* 1.3 81.0 + - + +
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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