Contacts of the helix formed by residues 304 - 316 (chain A) in PDB entry 3UJG
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 SER 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ARG* 3.5 6.3 - - - +
303A GLN* 1.3 76.9 - - - +
305A ILE* 1.3 67.1 + - - +
306A GLU* 3.7 16.1 + - - +
307A GLU* 3.1 37.7 + - - +
308A ILE* 3.1 13.8 + - - +
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Residues in contact with ILE 305 (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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67A ILE* 3.2 45.8 - - + -
70A ARG* 3.8 20.9 - - - +
304A SER* 1.3 73.8 - - - +
306A GLU* 1.3 62.5 + - + +
308A ILE* 3.4 5.2 + - + +
309A MET* 2.9 50.6 + - + +
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Residues in contact with GLU 306 (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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304A SER* 3.2 17.5 + - - +
305A ILE* 1.3 82.2 - - + +
307A GLU* 1.3 69.6 + - + +
309A MET* 3.9 6.0 - - - +
310A GLN* 2.9 32.8 + - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLN* 3.8 18.5 - - + +
304A SER* 3.1 30.2 + - - +
306A GLU* 1.3 86.4 - - + +
308A ILE* 1.3 61.1 + - - +
310A GLN* 3.4 7.8 + - - +
311A ILE* 3.1 35.7 + - + +
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 6.3 1.3 - - + -
66A ILE* 4.2 16.2 - - + -
67A ILE* 3.7 27.8 - - + -
70A ARG* 3.9 35.0 - - + +
80A PHE* 3.9 11.9 - - + -
83A VAL* 4.1 16.5 - - + +
303A GLN* 3.1 28.5 - - - +
304A SER 3.1 12.4 + - - +
305A ILE* 3.7 7.4 - - - +
307A GLU* 1.3 75.3 - - - +
309A MET* 1.3 59.6 + - + +
311A ILE* 3.4 2.1 + - - +
312A ILE* 3.0 31.8 + - + +
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Residues in contact with MET 309 (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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63A LYS* 3.6 48.2 - - + +
64A ARG* 5.6 2.0 - - - +
67A ILE* 5.1 4.0 - - - -
305A ILE* 2.9 42.2 + - + +
306A GLU* 3.9 6.3 - - - +
308A ILE* 1.3 75.8 - - - +
310A GLN* 1.3 63.0 + - - +
312A ILE* 3.0 22.3 - - + +
313A ALA* 3.2 11.4 + - - +
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Residues in contact with GLN 310 (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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306A GLU* 2.9 21.0 + - - +
307A GLU* 3.7 11.0 - - - +
309A MET* 1.3 76.5 - - - +
311A ILE* 1.3 58.7 + - + +
313A ALA* 3.4 10.6 - - - +
314A GLU* 3.2 30.4 + - - +
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Residues in contact with ILE 311 (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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83A VAL* 3.0 31.2 - - + +
84A ILE* 4.6 4.3 - - - -
85A LEU* 3.7 30.1 - - + +
90A LEU* 3.7 19.7 - - + -
303A GLN* 4.2 8.3 - - - +
307A GLU* 3.1 23.3 + - + +
308A ILE 3.4 3.6 + - - +
310A GLN* 1.3 76.6 - - + +
312A ILE* 1.3 60.9 + - - +
313A ALA 3.1 1.6 - - - -
314A GLU* 3.4 9.5 + - - +
315A ALA* 3.0 25.6 + - - +
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Residues in contact with ILE 312 (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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58A ILE* 3.2 27.3 - - + +
59A ASP 4.4 2.9 - - - +
62A VAL* 4.0 4.5 - - + -
63A LYS* 3.3 47.8 - - + +
66A ILE* 5.8 3.8 - - + -
83A VAL* 5.5 0.8 - - + +
90A LEU* 4.8 10.3 - - + -
308A ILE* 3.0 18.7 + - + +
309A MET* 3.0 42.8 - - + +
311A ILE* 1.3 78.2 - - - +
313A ALA* 1.3 62.2 + - - +
315A ALA* 3.4 16.4 + - - +
316A THR* 3.5 9.1 + - + +
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Residues in contact with ALA 313 (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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309A MET 3.2 14.6 + - - +
310A GLN* 3.4 18.4 - - - +
311A ILE 3.1 0.2 - - - -
312A ILE* 1.3 75.3 - - + +
314A GLU* 1.3 61.2 + - - +
315A ALA 3.0 4.3 + - - -
316A THR* 2.9 27.3 + - - -
317A VAL* 4.5 3.6 - - - +
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Residues in contact with GLU 314 (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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54A ARG* 3.2 24.7 + - - +
85A LEU* 3.2 32.1 - - + +
310A GLN* 3.2 20.2 + - - +
311A ILE* 3.4 7.9 + - - +
313A ALA* 1.3 79.2 - - - +
315A ALA* 1.3 58.7 + - - +
316A THR 3.4 0.2 - - - -
317A VAL* 3.7 14.9 + - + +
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Residues in contact with ALA 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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54A ARG* 2.9 33.9 - - + +
58A ILE* 3.4 17.2 - - + +
85A LEU* 4.1 18.6 - - + -
90A LEU* 4.3 17.5 - - + -
311A ILE 3.0 17.5 + - - +
312A ILE* 3.4 13.5 - - - +
313A ALA 3.0 0.6 - - - -
314A GLU* 1.3 74.7 - - - +
316A THR* 1.3 56.4 + - - +
317A VAL 3.1 6.1 - - - -
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Residues in contact with THR 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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54A ARG 4.0 2.5 - - - -
56A GLU* 3.4 45.2 + - - +
58A ILE* 3.6 25.4 - - + +
312A ILE* 3.6 11.2 - - + +
313A ALA* 2.9 19.0 + - - +
315A ALA* 1.3 76.1 - - - +
317A VAL* 1.3 62.5 + - - +
318A PRO* 3.3 11.6 - - - +
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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