Contacts of the helix formed by residues 319 - 335 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG* 2.8 56.4 + - + +
13A ILE* 4.1 7.2 - - + +
16A ASN* 3.7 15.7 + - - +
52A VAL* 4.1 6.7 - - - +
53A LEU* 5.5 0.9 - - - +
240A PRO 4.6 6.7 - - - +
241A ASN* 3.5 28.7 - - - +
317A ASP* 2.9 6.8 + - - +
318A ASN* 1.3 79.1 - - - +
320A TRP* 1.3 60.3 + - + +
321A GLY 3.6 0.2 - - - -
322A TYR* 3.8 1.0 - - - +
323A SER* 2.9 33.1 + - - -
1341A NAP 3.8 20.6 + - - +
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Residues in contact with TRP 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 3.5 18.8 + - - +
19A ARG* 4.0 27.1 - - + -
20A CYS* 3.7 37.1 - - - -
23A GLY* 6.3 0.9 - - - -
53A LEU* 3.4 31.6 - - + -
290A GLY* 3.5 19.4 + - - -
291A THR 3.6 15.5 - - - -
292A ASP* 2.7 27.3 + - - -
317A ASP* 2.8 25.3 + - - +
319A GLU* 1.3 72.2 - - + +
321A GLY* 1.3 65.9 + - - +
323A SER* 3.2 4.2 + - - -
324A GLN* 2.9 34.0 + - + +
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Residues in contact with GLY 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A THR 3.7 17.3 - - - -
292A ASP 4.0 9.2 - - - -
293A GLU 4.3 7.6 - - - -
294A SER* 5.4 3.4 - - - -
317A ASP* 2.9 19.8 + - - +
320A TRP* 1.3 76.1 - - - +
322A TYR* 1.3 62.8 + - - +
324A GLN* 3.1 14.1 + - - +
325A ARG* 3.2 19.2 + - - +
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Residues in contact with TYR 322 (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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13A ILE* 4.1 12.8 - - + -
122A THR* 2.9 41.6 - - - -
123A ALA 3.1 0.7 + - - -
152A ASN* 3.2 29.8 - - + +
153A ALA 2.5 28.5 + - - -
154A SER 3.5 13.5 - - - -
155A CYS* 3.6 19.3 - - + -
158A ASN* 4.1 7.6 - - + -
317A ASP 3.6 4.2 + - - -
318A ASN 3.2 21.8 - - - +
319A GLU 3.8 0.9 - - - +
320A TRP 3.2 0.4 - - - -
321A GLY* 1.3 75.7 - - - +
323A SER* 1.3 60.5 + - - +
325A ARG* 2.8 24.0 + - - +
326A VAL* 2.9 27.4 + - + +
1341A NAP 3.7 18.8 - + - -
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.6 15.8 + - - +
16A ASN* 3.2 17.8 - - - +
17A PHE* 3.6 21.9 + - - -
20A CYS* 3.8 11.2 - - - -
319A GLU 2.9 23.6 + - - -
320A TRP 3.2 4.9 + - - -
322A TYR* 1.3 75.2 - - - +
324A GLN* 1.3 56.4 + - - +
326A VAL* 3.3 11.4 - - - +
327A VAL* 2.9 32.9 + - - +
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Residues in contact with GLN 324 (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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20A CYS* 3.2 30.6 - - - +
24A ARG* 2.6 48.4 + - - +
292A ASP* 3.1 38.3 - - - +
320A TRP* 2.9 30.1 + - + +
321A GLY 3.1 9.6 + - - +
323A SER* 1.3 75.6 + - - +
325A ARG* 1.3 74.5 + - - +
327A VAL* 3.4 0.9 + - - +
328A ASP* 3.0 24.4 + - - -
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Residues in contact with ARG 325 (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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24A ARG* 5.1 1.0 - - - +
135A ILE* 3.8 25.8 - - + +
152A ASN* 3.7 10.3 - - - +
158A ASN* 3.3 23.6 - - + +
274A GLY 4.1 8.5 + - - -
275A ILE* 3.9 13.5 - - - +
292A ASP* 2.8 32.5 + - - +
293A GLU* 3.6 1.4 - - - +
294A SER* 2.8 45.6 + - - +
321A GLY 3.2 11.3 + - - +
322A TYR* 2.8 11.1 + - - +
324A GLN* 1.3 90.9 + - - +
326A VAL* 1.3 60.7 + - - +
327A VAL 3.1 1.3 - - - -
328A ASP* 2.8 31.3 + - - +
329A LEU* 2.8 30.0 + - - +
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Residues in contact with VAL 326 (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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13A ILE* 4.8 1.6 - - + -
17A PHE* 3.1 31.4 - - + -
96A ILE* 4.6 7.4 - - + -
120A LEU* 3.8 7.3 - - + +
122A THR* 4.2 22.0 - - + -
152A ASN* 3.7 17.7 - - + +
322A TYR* 2.9 39.8 + - + +
323A SER* 3.3 15.7 - - - +
325A ARG* 1.3 69.7 - - - +
327A VAL* 1.3 63.7 + - - +
329A LEU* 3.5 1.7 + - - -
330A ALA* 3.0 22.5 + - - +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.5 31.9 - - + +
20A CYS* 3.9 22.0 - - + -
21A TRP* 4.1 8.7 - - + +
24A ARG* 3.4 33.0 - - + +
29A LEU* 4.8 6.1 - - + -
323A SER 2.9 18.0 + - - +
324A GLN 3.5 8.3 - - - +
326A VAL* 1.3 75.6 - - - +
328A ASP* 1.3 52.5 + - - +
330A ALA* 2.9 5.1 + - - +
331A GLU* 2.8 51.6 + - + +
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Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.5 29.0 + - - +
135A ILE* 3.9 22.5 - - + +
275A ILE* 4.9 1.6 - - - +
324A GLN 3.0 13.9 + - - -
325A ARG* 2.8 40.4 + - - +
327A VAL* 1.3 74.6 - - - +
329A LEU* 1.3 55.6 + - - +
331A GLU* 3.3 10.0 + - - +
332A LEU* 2.8 27.9 + - - +
335A ARG* 4.8 2.4 + - - -
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.6 31.2 - - + -
133A TYR* 3.9 29.4 - - + -
135A ILE* 3.7 11.6 - - + +
142A TYR* 4.7 5.4 - - + -
150A ILE* 4.2 11.7 - - + -
151A SER 3.9 11.4 - - - +
152A ASN* 3.4 24.5 - - + +
325A ARG 2.8 19.5 + - - +
326A VAL 3.8 4.0 - - - +
328A ASP* 1.3 70.3 - - - +
330A ALA* 1.3 62.0 + - - +
332A LEU* 3.3 19.0 + - + +
333A ALA* 3.0 24.8 + - - +
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Residues in contact with ALA 330 (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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3A ILE* 4.4 1.2 - - - +
17A PHE* 4.6 0.9 - - + -
29A LEU* 3.9 21.8 - - + +
94A LEU* 3.7 26.9 - - + -
96A ILE* 4.3 8.7 - - + -
120A LEU* 3.9 8.7 - - + +
326A VAL 3.0 13.7 + - - +
327A VAL* 2.9 10.1 + - - +
329A LEU* 1.3 72.6 - - - +
331A GLU* 1.3 54.6 + - - +
333A ALA* 2.9 6.4 + - - +
334A ALA* 2.8 34.5 + - - +
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Residues in contact with GLU 331 (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 TRP* 4.5 1.0 - - - -
24A ARG* 5.1 6.5 + - - +
26A ASN 4.1 3.7 - - - +
27A THR* 2.4 35.1 + - - -
28A ASP* 3.1 27.5 + - - +
29A LEU* 3.9 10.8 - - + +
327A VAL* 2.8 33.5 + - + +
328A ASP* 3.4 11.2 - - - +
330A ALA* 1.3 79.0 - - - +
332A LEU* 1.3 56.2 + - - +
334A ALA* 3.3 6.6 + - - +
335A ARG* 3.0 48.4 + - - +
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Residues in contact with LEU 332 (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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133A TYR* 5.8 0.7 - - + -
135A ILE* 4.5 4.9 - - + -
139A ASP* 3.9 32.5 - - + +
142A TYR* 3.9 27.1 - - + -
328A ASP 2.8 13.6 + - - +
329A LEU* 3.4 22.9 - - + +
331A GLU* 1.3 73.3 - - - +
333A ALA* 1.3 66.8 + - - +
335A ARG* 3.2 26.7 + - - +
336A LYS* 3.0 48.6 - - + +
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Residues in contact with ALA 333 (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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3A ILE* 4.8 3.8 - - + -
94A LEU* 4.8 10.5 - - + -
118A LYS* 4.7 11.0 - - + -
142A TYR* 3.5 29.6 - - + +
144A HIS* 4.7 3.4 - - + -
150A ILE* 4.9 5.2 - - + -
329A LEU 3.0 12.8 + - - +
330A ALA* 2.9 13.3 + - - +
332A LEU* 1.3 76.0 - - - +
334A ALA* 1.3 63.8 + - - +
336A LYS* 3.0 21.8 + - - +
337A SER* 3.5 4.9 + - - -
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Residues in contact with ALA 334 (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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1A MET* 5.0 10.4 + - - +
3A ILE* 3.8 38.2 - - + +
28A ASP* 3.7 27.8 - - + +
29A LEU* 4.1 4.3 - - + -
330A ALA 2.8 11.9 + - - +
331A GLU 3.3 10.3 - - - +
333A ALA* 1.3 73.4 - - - +
335A ARG* 1.3 54.4 + - - +
336A LYS 2.5 19.2 + - - -
337A SER* 3.5 7.1 + - - -
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Residues in contact with ARG 335 (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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1A MET 5.8 2.5 - - - +
28A ASP* 3.5 22.6 + - - +
328A ASP 4.8 2.8 + - - -
331A GLU* 3.0 32.4 + - - +
332A LEU* 3.2 33.6 + - - +
334A ALA* 1.3 74.4 - - - +
336A LYS* 1.3 80.4 + - - +
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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
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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