Contacts of the helix formed by residues 314 - 325 (chain A) in PDB entry 3IO6
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 ASP 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A TRP* 4.9 0.5 - - - -
311A LEU 3.1 10.4 + - - +
312A ALA 3.6 3.3 - - - +
313A LYS* 1.3 76.5 - - - +
315A PRO* 1.3 76.8 - - - +
316A ARG* 2.9 48.5 + - - +
317A ILE* 3.0 38.6 + - + +
318A ALA 3.4 7.6 + - - -
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Residues in contact with PRO 315 (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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119A LYS* 6.1 2.5 - - - +
244A VAL 4.1 9.5 - - - +
312A ALA 4.7 1.3 - - - +
313A LYS 3.4 9.8 - - - +
314A ASP* 1.3 89.8 - - - +
316A ARG* 1.3 61.8 + - + +
318A ALA* 3.5 7.6 + - + +
319A ALA* 3.1 28.2 + - - +
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Residues in contact with ARG 316 (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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232A TRP* 3.6 44.8 - - + +
236A ASP* 4.6 7.1 + - - -
242A TYR* 2.8 40.7 + - + -
243A GLY* 5.5 1.3 - - - -
244A VAL* 3.8 27.7 - - + +
314A ASP* 2.9 29.4 + - - +
315A PRO* 1.3 79.3 - - + +
317A ILE* 1.3 64.9 + - - +
319A ALA* 3.3 4.2 + - - +
320A THR* 3.2 24.8 + - - -
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Residues in contact with ILE 317 (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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232A TRP* 4.2 18.6 - - + -
294A ASN* 6.1 0.7 - - - +
298A PRO* 6.3 2.2 - - + -
300A GLY* 3.7 30.5 - - - +
301A ALA* 3.9 13.0 - - + +
308A GLU* 4.3 6.0 - - - +
311A LEU* 3.8 44.6 - - + +
314A ASP* 3.0 29.3 + - + +
316A ARG* 1.3 76.3 - - - +
318A ALA* 1.3 62.6 + - - +
320A THR* 3.4 6.1 + - - -
321A MET* 3.3 20.8 + - - +
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Residues in contact with ALA 318 (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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308A GLU* 4.6 3.6 - - - -
312A ALA* 3.4 39.0 - - + +
314A ASP 3.4 3.0 + - - +
315A PRO* 3.8 10.1 - - + +
316A ARG 3.3 0.2 - - - -
317A ILE* 1.3 78.6 - - - +
319A ALA* 1.3 57.9 + - - +
321A MET* 3.7 3.3 + - - +
322A GLU* 3.1 26.5 + - - +
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Residues in contact with ALA 319 (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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114A SER* 4.3 0.2 - - - -
244A VAL* 3.6 33.0 - - + +
245A THR* 3.8 12.1 - - - -
246A VAL 4.5 0.7 - - - +
315A PRO 3.1 16.5 + - - +
316A ARG 3.5 6.3 - - - +
317A ILE 3.2 0.2 - - - -
318A ALA* 1.3 75.4 - - - +
320A THR* 1.3 59.4 + - - +
322A GLU* 3.3 6.5 + - - +
323A ASN* 2.9 36.6 + - - -
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Residues in contact with THR 320 (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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110A VAL* 4.1 15.7 - - + +
112A ALA* 3.6 35.0 - - + +
114A SER* 3.7 14.3 + - - -
229A PRO* 4.2 11.3 - - + +
232A TRP* 3.6 19.0 - - - -
301A ALA* 4.7 7.0 - - + +
316A ARG 3.2 11.8 + - - -
317A ILE* 3.4 10.3 + - - -
319A ALA* 1.3 78.9 - - - +
321A MET* 1.3 55.7 + - - +
323A ASN* 3.6 3.4 + - - +
324A ALA* 3.1 25.6 + - - +
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Residues in contact with MET 321 (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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90A TYR* 4.4 15.0 - - + +
92A PHE* 3.8 27.4 - - + -
110A VAL* 4.1 14.6 - - + -
301A ALA* 3.7 21.7 - - + +
302A VAL 3.4 25.6 - - - +
303A ALA* 5.2 0.2 - - - -
308A GLU* 3.8 30.3 - - + +
317A ILE 3.3 8.6 + - - +
318A ALA* 4.0 4.3 - - - +
319A ALA 3.3 0.6 - - - -
320A THR* 1.3 77.1 - - - +
322A GLU* 1.3 65.2 + - - +
324A ALA* 3.1 6.2 + - - +
325A GLN* 3.0 38.6 + - - +
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Residues in contact with GLU 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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246A VAL* 3.7 27.8 - - + +
318A ALA 3.1 19.1 + - - +
319A ALA* 3.5 7.9 - - - +
321A MET* 1.3 79.0 - - - +
323A ASN* 1.3 60.7 + - - +
324A ALA 3.4 0.2 + - - -
325A GLN* 3.7 16.2 + - - +
326A LYS* 3.2 48.4 + - - +
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Residues in contact with ASN 323 (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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112A ALA* 4.6 1.6 - - + -
113A LEU 3.3 20.4 - - - +
114A SER* 3.2 29.5 + - - +
245A THR 3.4 12.3 + - - -
246A VAL* 3.4 10.9 - - - +
247A LEU* 3.0 33.9 + - - +
255A SER 5.4 1.0 - - - +
257A PRO* 3.6 16.5 - - + +
319A ALA 2.9 23.1 + - - +
320A THR 3.8 5.4 - - - +
322A GLU* 1.3 76.7 - - - +
324A ALA* 1.3 60.5 + - - +
326A LYS* 3.5 6.2 + - - +
327A GLY 3.2 15.4 + - - -
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Residues in contact with ALA 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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92A PHE* 4.1 16.0 - - + -
110A VAL* 3.6 29.4 - - + -
112A ALA* 4.2 7.0 - - + -
259A VAL* 3.8 14.6 - - + +
320A THR 3.1 15.7 + - - +
321A MET* 3.1 11.4 + - - +
323A ASN* 1.3 73.2 - - - +
325A GLN* 1.3 56.0 + - - +
326A LYS 2.7 5.4 + - - -
327A GLY* 2.7 30.5 + - - +
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Residues in contact with GLN 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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90A TYR* 3.7 24.4 - - - -
91A PRO* 6.0 0.2 - - - +
92A PHE* 3.6 34.2 - - + +
321A MET* 3.0 30.6 + - - +
322A GLU* 4.2 21.1 + - - +
323A ASN 3.6 0.2 - - - -
324A ALA* 1.3 74.4 - - - +
326A LYS* 1.3 62.7 + - + +
327A GLY 3.5 2.7 - - - +
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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
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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