Contacts of the helix formed by residues 305 - 311 (chain P) in PDB entry 3EXG
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 ALA 305 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111M GLY* 4.2 11.7 - - - +
119M GLY 2.9 20.0 + - - +
329M GLU* 4.4 4.3 - - - +
330M PRO* 3.7 33.4 - - + -
303P PRO 3.8 0.2 - - - -
304P TYR* 1.3 81.4 - - - +
306P LYS* 1.3 56.1 + - - +
307P ILE* 4.7 0.2 - - + -
308P LEU* 3.1 14.7 + - + +
309P GLU* 2.8 32.1 + - - +
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Residues in contact with LYS 306 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ARG* 3.6 47.5 - - - +
111M GLY 5.4 0.2 + - - -
329M GLU* 3.6 13.3 + - - +
304P TYR 3.3 2.4 + - - -
305P ALA* 1.3 70.9 - - - +
307P ILE* 1.3 60.6 + - - +
309P GLU* 3.3 1.8 + - - +
310P ASP* 2.8 67.7 + - - +
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Residues in contact with ILE 307 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329M GLU* 3.1 31.0 + - + +
330M PRO 4.0 19.3 - - - +
332M LEU* 4.4 20.4 - - + +
305P ALA* 4.7 1.8 - - + -
306P LYS* 1.3 79.6 - - - +
308P LEU* 1.3 72.4 + - + +
310P ASP* 3.5 7.4 + - + +
311P ASN* 2.8 43.8 + - - +
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Residues in contact with LEU 308 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M GLY 4.4 1.1 - - - +
120M LYS* 3.7 33.7 - - + -
330M PRO* 3.8 24.7 - - + -
331M PRO 4.1 18.2 - - - +
332M LEU* 4.1 11.9 - - + +
334M GLU 5.0 0.9 - - - +
335M LEU* 3.0 38.3 - - + +
303P PRO* 3.4 16.6 - - + -
305P ALA* 3.1 18.8 + - + +
306P LYS 3.1 0.4 - - - -
307P ILE* 1.3 82.2 - - + +
309P GLU* 1.3 64.3 + - - +
311P ASN 3.4 5.4 + - - -
312P SER* 2.8 20.3 + - - -
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Residues in contact with GLU 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M ARG* 3.2 30.3 + - - +
121P SER 4.8 2.8 - - - +
122P ALA* 3.6 12.8 + - - +
123P GLY* 2.7 27.3 + - - -
124P VAL 4.3 2.3 + - - -
125P ALA 5.3 0.2 + - - -
129P SER* 5.5 1.0 + - - -
302P MET* 4.1 16.7 - - - +
303P PRO* 3.8 18.9 - - - +
305P ALA 2.8 16.4 + - - +
306P LYS* 3.8 3.2 - - - +
308P LEU* 1.3 76.7 - - - +
310P ASP* 1.3 71.2 + - - +
312P SER* 3.0 21.9 + - - -
313P ILE* 3.8 20.2 - - + +
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Residues in contact with ASP 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306P LYS* 2.8 62.9 + - - +
307P ILE* 3.6 10.0 - - + +
308P LEU 3.3 0.2 - - - -
309P GLU* 1.3 78.1 - - - +
311P ASN* 1.3 60.7 + - - +
312P SER 3.3 2.9 + - - -
313P ILE* 3.6 11.4 + - - +
315P GLN* 3.4 28.7 - - + +
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Residues in contact with ASN 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332M LEU* 3.3 37.8 - - + +
335M LEU* 4.3 6.2 - - + +
351M ALA* 4.9 8.0 + - - +
357M PHE* 4.5 14.2 - - + -
298P ALA* 3.7 12.0 - - - +
307P ILE* 2.8 33.6 + - - +
308P LEU 3.4 3.3 + - - +
309P GLU 3.2 1.0 - - - -
310P ASP* 1.3 78.9 - - - +
312P SER* 1.3 61.7 + - - +
313P ILE 3.5 3.6 - - - -
315P GLN* 3.9 19.8 + - - +
317P LYS* 5.8 2.1 + - - -
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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