Contacts of the helix formed by residues 268 - 286 (chain 5) 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 PRO 268 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2695 GLY* 1.3 58.4 + - - +
2705 VAL* 2.4 23.9 + - + +
2715 ALA* 2.3 53.9 + - + +
2725 TYR 3.1 0.7 + - - -
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Residues in contact with GLY 269 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2685 PRO* 1.3 79.6 - - - +
2705 VAL* 1.3 51.4 + - - +
2725 TYR* 3.1 10.7 + - - +
2735 ARG* 2.3 61.0 + - - -
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Residues in contact with VAL 270 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2685 PRO* 2.4 27.0 + - + +
2695 GLY* 1.3 64.9 - - - +
2715 ALA* 1.3 66.4 + - - +
2725 TYR 2.8 2.3 + - - -
2735 ARG* 3.0 25.3 + - - +
2745 THR* 2.3 48.2 + - + +
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Residues in contact with ALA 271 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2685 PRO* 2.3 38.7 + - + +
2705 VAL* 1.3 84.2 - - - +
2725 TYR* 1.3 58.0 + - - +
2745 THR* 3.3 6.1 + - - -
2755 ARG* 3.2 29.3 + - + +
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Residues in contact with TYR 272 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2685 PRO 3.1 1.0 + - - +
2695 GLY* 3.1 13.3 + - - +
2705 VAL 2.8 5.7 + - - -
2715 ALA* 1.3 71.1 - - - +
2735 ARG* 1.3 83.1 + - + +
2745 THR 3.0 1.8 - - - -
2755 ARG* 3.0 23.2 + - + +
2765 GLU* 3.1 48.8 + - + +
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Residues in contact with ARG 273 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2695 GLY* 2.3 72.3 + - - +
2705 VAL* 3.2 22.7 + - - +
2725 TYR* 1.3 87.2 - - + +
2745 THR* 1.3 64.1 + - + +
2765 GLU* 3.3 5.0 + - - +
2775 GLU* 3.2 19.6 + - - +
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Residues in contact with THR 274 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2705 VAL* 2.3 53.2 - - + +
2715 ALA* 3.3 5.7 + - - +
2735 ARG* 1.3 75.9 - - + +
2755 ARG* 1.3 69.1 + - - +
2775 GLU* 3.0 19.4 + - - +
2785 ILE* 2.9 28.6 + - - +
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Residues in contact with ARG 275 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2715 ALA* 3.2 21.9 + - - +
2725 TYR* 3.0 15.5 + - + +
2745 THR* 1.3 85.1 + - - +
2765 GLU* 1.3 65.0 + - + +
2785 ILE* 3.4 16.0 - - - +
2795 GLN* 3.0 21.0 + - - +
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Residues in contact with GLU 276 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2725 TYR* 3.1 51.2 + - + +
2735 ARG* 3.8 7.4 - - - +
2755 ARG* 1.3 75.3 - - - +
2775 GLU* 1.3 67.1 - - - +
2795 GLN* 3.1 17.9 + - - +
2805 GLU* 3.0 21.3 + - - +
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Residues in contact with GLU 277 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1975 ARG* 3.1 31.8 + - - +
2585 TYR* 3.9 12.5 + - - +
2735 ARG 3.2 12.0 + - - +
2745 THR* 3.0 13.7 + - - +
2765 GLU* 1.3 77.4 - - - +
2785 ILE* 1.3 52.1 + - - +
2805 GLU* 3.0 22.8 - - + +
2815 VAL* 2.6 28.2 - - - +
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Residues in contact with ILE 278 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2585 TYR* 3.2 20.6 + - + +
2595 ARG 5.0 0.7 - - - +
2605 TYR* 3.7 51.1 - - + +
2745 THR* 2.9 28.5 - - - +
2755 ARG* 3.4 16.8 - - - +
2775 GLU* 1.3 73.8 - - - +
2795 GLN* 1.3 72.2 + - - +
2815 VAL* 3.8 3.0 - - - +
2825 ARG* 2.8 37.5 + - - +
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Residues in contact with GLN 279 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2755 ARG 3.0 10.3 + - - +
2765 GLU* 3.2 24.5 - - - +
2785 ILE* 1.3 80.7 - - - +
2805 GLU* 1.3 60.6 + - - +
2825 ARG* 3.3 26.0 - - - +
2835 SER* 2.3 60.6 + - - -
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Residues in contact with GLU 280 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1975 ARG* 5.7 3.3 + - - -
2765 GLU 3.0 11.5 + - - +
2775 GLU* 3.0 17.3 - - + +
2795 GLN* 1.3 82.0 - - - +
2815 VAL* 1.3 69.5 + - - +
2835 SER* 2.7 13.8 + - - -
2845 LYS* 2.8 45.7 + - + +
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Residues in contact with VAL 281 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1975 ARG* 4.6 8.5 - - - +
2285 MET* 4.5 9.9 - - + -
2585 TYR* 3.6 55.6 - - + -
2605 TYR* 4.7 2.5 - - + -
2775 GLU* 2.6 25.6 - - + +
2785 ILE* 3.8 2.9 - - - +
2805 GLU* 1.3 76.5 + - + +
2825 ARG* 1.3 69.0 + - - +
2845 LYS* 4.7 2.2 - - - +
2855 SER* 2.6 35.5 + - - +
2865 ASP 3.3 2.0 + - - -
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Residues in contact with ARG 282 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435 ARG* 5.0 7.1 - - - +
665 ASP* 5.3 1.2 + - - -
2605 TYR* 3.3 52.3 + - + +
2785 ILE* 2.8 39.5 + - - +
2795 GLN* 3.3 23.4 - - - +
2805 GLU 2.8 1.2 + - - -
2815 VAL* 1.3 82.3 - - - +
2835 SER* 1.3 59.1 + - - +
2845 LYS 2.5 10.9 + - - -
2855 SER 2.7 7.8 + - - -
2865 ASP* 2.8 26.8 + - + +
2895 MET* 4.3 1.7 - - - +
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Residues in contact with SER 283 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2795 GLN* 2.3 46.0 + - - -
2805 GLU* 2.7 10.6 + - - -
2825 ARG* 1.3 79.3 - - - +
2845 LYS* 1.3 58.1 + - - +
2895 MET* 4.2 15.7 - - - +
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Residues in contact with LYS 284 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2805 GLU* 2.8 48.0 + - + +
2815 VAL* 4.3 2.9 - - - +
2825 ARG 2.5 10.0 + - - -
2835 SER* 1.3 75.3 - - - +
2855 SER* 1.3 66.3 + - - +
2895 MET* 3.8 9.8 - - - +
2905 LEU* 3.9 4.9 - - - +
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Residues in contact with SER 285 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2285 MET* 3.4 32.8 - - - +
2815 VAL* 2.6 33.3 + - - +
2825 ARG 2.7 3.2 + - - -
2845 LYS* 1.3 82.9 + - - +
2865 ASP* 1.3 67.1 + - - +
2875 PRO 3.2 1.9 - - - -
2895 MET* 3.8 5.8 - - - -
2905 LEU* 3.7 18.3 - - - +
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Residues in contact with ASP 286 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435 ARG* 2.9 35.2 + - - -
2605 TYR* 2.9 22.3 + - - +
2815 VAL 3.3 1.6 + - - -
2825 ARG* 2.8 32.5 + - + +
2855 SER* 1.3 71.6 - - - +
2875 PRO* 1.3 70.1 - - - +
2885 ILE* 2.9 28.6 + - - +
2895 MET* 3.0 23.1 + - + +
2905 LEU* 3.0 21.3 + - - +
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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