Contacts of the helix formed by residues 308 - 318 (chain E) in PDB entry 3Q3G
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 ILE 308 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E PHE* 4.3 6.5 - - + -
269E ILE* 3.8 47.3 - - + -
297E PHE* 3.8 32.1 - - + -
298E GLN 5.0 4.0 - - - +
299E VAL* 3.8 24.5 - - + -
305E LEU* 3.6 13.7 - - + +
306E LYS 3.4 0.2 - - - -
307E THR* 1.3 79.7 - - + +
309E GLN* 1.3 63.5 + - - +
310E ASN 3.4 2.2 - - - -
311E GLN* 3.8 16.2 - - - +
312E LEU* 3.0 28.8 + - + +
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Residues in contact with GLN 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E PHE* 3.3 52.4 + - - +
159E THR* 3.5 25.6 - - + +
160E VAL* 3.4 14.9 - - + +
163E GLN* 3.9 24.8 + - - +
305E LEU 3.6 2.8 + - - -
306E LYS* 3.2 29.5 + - - +
307E THR 3.4 0.8 - - - -
308E ILE* 1.3 75.7 - - - +
310E ASN* 1.4 66.3 + - - +
312E LEU* 4.1 1.9 - - - +
313E ARG* 3.2 23.7 + - - +
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Residues in contact with ASN 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 4.2 24.4 + - - +
163E GLN* 5.1 1.7 + - - +
306E LYS 4.4 4.0 + - - -
307E THR 4.4 5.1 + - - -
308E ILE 3.4 0.2 - - - -
309E GLN* 1.4 82.3 - - - +
311E GLN* 1.4 70.1 + - - +
313E ARG* 3.4 33.1 + - - +
314E GLU* 3.0 36.6 + - + +
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Residues in contact with GLN 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E PHE* 3.8 20.4 - - + -
307E THR* 2.7 33.8 + - - +
308E ILE* 3.5 15.1 + - - +
310E ASN* 1.4 85.1 - - - +
312E LEU* 1.4 59.5 + - - +
314E GLU* 3.7 5.8 + - - +
315E LYS* 3.1 35.3 + - - +
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Residues in contact with LEU 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E PHE* 3.7 27.6 - - + -
160E VAL* 4.2 21.5 - - + -
238E VAL* 4.2 18.6 - - + -
267E TYR* 4.2 14.4 - - + -
269E ILE* 4.2 10.8 - - + -
297E PHE* 3.7 30.9 - - + -
308E ILE* 3.0 19.5 + - + +
309E GLN 4.1 2.2 - - - +
311E GLN* 1.4 72.7 - - - +
313E ARG* 1.4 66.4 + - - +
315E LYS* 3.2 3.3 + - - +
316E ILE* 3.0 49.2 + - + +
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Residues in contact with ARG 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E VAL* 5.9 4.2 - - + +
163E GLN* 2.8 58.6 + - + +
164E LEU* 3.7 21.5 - - + +
309E GLN 3.2 16.6 + - - +
310E ASN* 3.4 41.5 + - - +
312E LEU* 1.4 77.6 - - - +
314E GLU* 1.3 92.4 + - - +
316E ILE* 3.5 0.8 + - - -
317E PHE* 3.2 51.5 + - + -
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Residues in contact with GLU 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ASN* 3.0 21.4 + - + +
311E GLN* 4.0 6.1 - - - +
312E LEU 3.3 0.2 - - - -
313E ARG* 1.3 107.3 + - - +
315E LYS* 1.4 63.1 + - - +
317E PHE* 3.5 19.0 + - - +
318E ALA* 3.2 22.2 + - - +
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Residues in contact with LYS 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E TYR* 3.1 25.6 + - + +
293E ARG 3.0 26.6 + - - -
294E ASP* 3.4 26.9 - - - +
296E VAL 4.3 7.3 + - - -
297E PHE* 3.7 33.1 - - + -
311E GLN* 3.1 19.7 + - - +
312E LEU* 3.2 6.0 + - - +
314E GLU* 1.4 74.1 - - + +
316E ILE* 1.4 59.4 + - - +
318E ALA* 3.1 27.3 + - - +
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Residues in contact with ILE 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ILE* 3.8 29.6 - - + -
164E LEU* 3.8 32.1 - - + -
166E LYS* 4.8 2.2 - - - +
236E ILE* 3.8 24.7 - - + +
238E VAL* 4.4 8.3 - - + -
267E TYR* 3.7 32.3 - - + -
312E LEU* 3.0 32.6 + - + +
313E ARG 3.8 0.2 - - - +
315E LYS* 1.4 72.9 - - - +
317E PHE* 1.4 62.5 + - - +
318E ALA 3.4 5.2 - - - +
319E ILE 4.2 0.2 - - - +
320E GLU 3.2 28.8 - - - +
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Residues in contact with PHE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLN 3.8 14.8 - - - -
164E LEU* 3.5 17.0 - - + -
166E LYS* 3.6 34.8 - - + +
313E ARG* 3.2 48.7 + - + +
314E GLU* 3.7 22.9 - - - +
316E ILE* 1.4 74.4 - - - +
318E ALA* 1.4 60.7 + - - +
319E ILE 3.4 2.6 + - - -
320E GLU* 3.4 19.8 + - - +
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Residues in contact with ALA 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E TYR* 4.8 1.7 + - - -
314E GLU 3.2 13.1 + - - +
315E LYS* 3.1 22.4 - - - +
316E ILE 3.3 3.5 - - - +
317E PHE* 1.4 71.1 - - - +
319E ILE* 1.3 76.7 + - + +
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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