Contacts of the helix formed by residues 327 - 344 (chain A) in PDB entry 2OOR
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 VAL 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.8 27.8 - - + +
146A TYR* 4.8 4.5 - - + -
147A ARG* 3.7 34.1 - - + -
323A VAL 4.0 5.8 - - - +
324A PRO 3.0 9.6 + - - +
326A ARG* 1.3 81.7 - - - +
328A ALA* 1.3 55.3 + - - +
330A ASP* 3.2 11.3 + - + -
331A ALA* 2.8 25.1 + - - +
157B ALA 3.1 17.0 - - - +
158B ARG* 3.9 3.6 - - - -
159B ALA* 3.7 29.6 - - + +
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 3.7 36.3 - - + +
15A ARG* 3.8 10.5 - - + -
42A GLY 3.9 7.4 - - - +
43A ALA* 3.8 2.5 - - - +
324A PRO 3.9 5.2 - - - -
325A SER 3.3 18.0 + - - +
326A ARG 3.6 0.8 - - - -
327A VAL* 1.3 75.8 - - - +
329A ALA* 1.3 57.5 + - - +
331A ALA* 3.8 0.7 - - - -
332A SER* 2.9 35.3 + - - -
157B ALA* 3.3 5.8 + - + +
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 3.1 34.1 - - - +
44A SER* 4.5 7.9 - - - -
45A ILE* 5.8 0.2 - - - +
328A ALA* 1.3 78.3 - - - +
330A ASP* 1.3 60.5 + - - +
333A PRO* 3.2 21.3 - - - +
157B ALA* 3.1 15.0 + - + +
158B ARG* 3.3 28.8 - - + +
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Residues in contact with ASP 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.7 15.0 - - + +
327A VAL* 3.2 12.1 + - + +
329A ALA* 1.3 74.9 - - - +
331A ALA* 1.3 66.1 + - - +
332A SER 3.3 2.2 + - - -
333A PRO* 3.5 6.5 - - - +
334A LEU* 3.4 22.5 - - - +
157B ALA 3.8 1.6 + - - -
158B ARG* 3.1 32.2 + - - +
159B ALA* 2.8 34.5 + - - +
161B PRO 5.5 0.2 - - - +
170B VAL* 3.6 37.7 - - + +
171B PRO* 5.0 0.9 - - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.7 10.1 - - - -
140A GLN* 3.1 34.1 + - - +
143A LEU* 3.4 16.5 - - + +
324A PRO 3.5 16.4 - - - +
327A VAL 2.8 18.0 + - - +
328A ALA 4.0 2.0 - - - +
330A ASP* 1.3 78.4 - - - +
332A SER* 1.3 56.2 + - - +
334A LEU* 3.6 1.5 + - - +
335A PHE* 3.0 25.1 + - - +
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.2 10.6 - - - +
16A VAL* 2.8 47.0 + - - +
18A ILE 4.5 2.5 - - - -
43A ALA* 3.8 12.4 - - - +
45A ILE* 4.9 0.2 - - - -
328A ALA 2.9 21.9 + - - -
331A ALA* 1.3 74.1 - - - +
333A PRO* 1.4 66.2 - - - +
335A PHE* 3.2 4.3 + - - +
336A ALA* 2.9 31.1 + - - +
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Residues in contact with PRO 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE 4.6 0.4 - - - -
19A SER* 4.1 31.8 + - - +
45A ILE* 4.8 9.2 - - + -
329A ALA 3.2 25.4 - - - +
330A ASP* 3.5 8.3 - - - +
332A SER* 1.4 93.0 - - - +
334A LEU* 1.3 55.8 + - + +
336A ALA* 3.7 3.1 + - + +
337A LYS* 3.1 40.6 + - - +
170B VAL* 5.3 7.2 - - + -
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 4.2 23.8 - - - +
140A GLN* 4.5 0.7 - - - +
142A ASN* 5.9 1.6 - - - +
143A LEU* 4.1 24.0 - - + -
330A ASP 3.4 17.3 - - - +
331A ALA 3.6 6.0 + - - +
332A SER 3.2 0.8 - - - -
333A PRO* 1.3 73.9 - - + +
335A PHE* 1.3 60.8 + - - +
337A LYS* 3.4 9.5 + - - +
338A ASN* 3.0 33.9 + - - -
165B THR* 3.9 14.6 - - + +
167B ALA* 3.7 16.1 - - + +
168B GLY 3.7 27.8 - - - +
169B THR 4.6 0.4 - - - +
170B VAL* 4.0 24.9 - - + +
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Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.8 26.2 - - - +
16A VAL 4.9 2.5 - - - +
17A ALA* 4.4 2.0 - - + -
73A LYS 3.6 20.9 - - - -
74A VAL* 3.7 35.4 - - + -
98A CYS 4.7 0.9 - - - -
99A HIS* 4.0 17.0 - + + -
136A ILE* 3.6 35.2 - - + -
140A GLN* 3.9 13.4 - - + +
331A ALA 3.0 18.7 + - - +
332A SER* 3.2 7.4 + - - +
334A LEU* 1.3 73.0 - - - +
336A ALA* 1.3 66.0 + - - +
338A ASN* 3.4 10.3 + - - +
339A LEU* 3.3 37.2 + - + +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 3.8 4.0 - - - +
18A ILE* 3.6 35.0 - - - +
22A VAL* 4.0 15.9 - - + +
72A TRP* 3.9 5.1 - - - -
332A SER 2.9 16.8 + - - +
333A PRO* 3.7 5.8 - - + +
335A PHE* 1.3 77.6 - - - +
337A LYS* 1.3 56.6 + - - +
339A LEU* 3.3 15.0 + - - +
340A LEU* 3.0 25.5 + - - +
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 5.5 1.3 - - - -
21A GLU* 3.8 31.6 - - - +
22A VAL* 4.2 15.0 - - + +
133A SER 4.4 0.7 - - - -
333A PRO* 3.1 32.7 + - - +
334A LEU* 3.9 7.0 - - - +
335A PHE 3.3 0.2 - - - -
336A ALA* 1.3 74.0 - - - +
338A ASN* 1.3 59.2 + - - +
340A LEU* 4.1 13.9 - - + -
341A ASN* 3.0 47.0 + - - +
167B ALA 2.9 36.1 + - - +
168B GLY* 3.8 14.2 - - - -
169B THR 4.8 3.6 + - - +
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Residues in contact with ASN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET* 4.0 2.4 - - - +
132A GLN 4.2 0.3 - - - +
133A SER 3.0 21.0 - - - +
134A MET* 3.3 28.0 - - - +
135A ASP 3.3 23.8 + - - +
136A ILE* 3.6 21.3 - - + +
139A SER* 2.8 32.5 + - - -
334A LEU 3.0 22.0 + - - -
335A PHE* 3.5 9.9 - - - +
337A LYS* 1.3 77.4 - - - +
339A LEU* 1.3 60.3 + - - +
342A PHE* 3.3 7.6 + - - +
167B ALA* 3.3 10.2 - - - +
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Residues in contact with LEU 339 (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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17A ALA* 3.8 19.7 - - + -
72A TRP* 3.6 31.8 + - + -
73A LYS 4.3 1.6 - - - +
97A MET* 3.7 36.3 - - + +
98A CYS 4.4 0.2 - - - +
122A MET* 3.8 28.7 - - + -
136A ILE* 5.6 0.4 - - + -
335A PHE* 3.3 38.7 + - + +
336A ALA* 3.5 7.0 - - - +
337A LYS 3.3 0.4 - - - -
338A ASN* 1.3 76.1 - - + +
340A LEU* 1.3 59.6 + - - +
342A PHE* 3.3 4.2 + - - +
343A LEU* 2.9 31.4 + - - +
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Residues in contact with LEU 340 (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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22A VAL* 4.2 20.4 - - + -
25A LYS* 3.8 34.3 - - + -
26A LEU* 4.2 21.5 - - + -
29A LEU* 4.0 18.2 - - + -
72A TRP* 3.5 10.9 - - + -
336A ALA 3.0 16.9 + - - +
337A LYS* 3.4 15.0 + - + +
339A LEU* 1.3 73.3 - - - +
341A ASN* 1.3 60.0 + - - +
343A LEU* 3.2 2.2 + - + -
344A THR* 2.6 58.4 + - - +
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Residues in contact with ASN 341 (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 SER* 3.0 49.6 + - - +
134A MET* 3.4 18.9 - - + +
337A LYS* 3.0 31.6 + - - +
340A LEU* 1.3 81.6 - - - +
342A PHE* 1.3 59.8 + - - +
344A THR* 4.6 4.9 + - - -
345A PRO* 3.3 16.9 - - - +
166B ALA 4.6 1.6 + - - -
167B ALA* 4.6 6.5 - - - +
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Residues in contact with PHE 342 (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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97A MET* 3.6 33.0 - - + -
120A TYR* 4.1 8.5 - + + -
122A MET* 3.8 24.0 - - + -
125A MET* 3.8 9.4 - - + -
134A MET* 3.7 11.5 - - + +
338A ASN 3.3 14.7 + - - +
339A LEU 3.3 7.1 + - - +
340A LEU 3.2 0.6 - - - -
341A ASN* 1.3 76.9 - - - +
343A LEU* 1.3 56.7 + - - +
345A PRO* 3.6 4.2 - - - +
346A HIS* 3.2 27.9 + - - -
356A MET* 3.6 26.7 - - + -
362A THR* 3.5 37.0 - - + +
363A VAL* 4.3 4.3 - - + -
366A THR* 3.6 31.0 - - + -
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Residues in contact with LEU 343 (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* 5.2 1.8 - - + -
26A LEU* 4.6 7.0 - - + -
29A LEU* 4.3 9.4 - - + -
31A PHE* 4.1 16.6 - - + -
70A VAL* 4.3 8.7 - - + -
72A TRP* 3.8 22.9 - - + +
97A MET* 3.8 23.6 - - + -
339A LEU 2.9 16.7 + - - +
340A LEU* 3.9 2.2 - - + +
342A PHE* 1.3 81.6 - - - +
344A THR* 1.3 66.1 + - - +
346A HIS* 3.0 24.8 + - - +
347A VAL* 3.4 27.2 + - + -
354A LEU* 3.7 24.9 - - + -
356A MET* 5.1 0.2 - - - -
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Residues in contact with THR 344 (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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29A LEU* 3.9 23.7 - - + +
340A LEU* 2.6 50.6 + - - +
341A ASN* 4.7 4.3 + - - -
343A LEU* 1.3 76.4 - - - +
345A PRO* 1.4 62.8 - - + +
346A HIS 3.1 6.1 + - - -
347A VAL* 3.5 16.0 + - - +
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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