Contacts of the helix formed by residues 270 - 282 (chain 6) 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 GLY 270 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1384 HIS* 4.3 1.1 - - - -
2694 PHE* 3.3 9.9 - - - +
1346 ALA* 3.9 9.4 - - - -
2636 GLU* 4.1 5.2 - - - -
2666 TRP 4.1 12.1 - - - -
2676 PRO 3.4 10.9 + - - -
2686 GLN 3.2 3.0 - - - -
2696 PHE* 1.3 83.0 - - - +
2716 VAL* 1.3 66.2 + - - -
2726 GLY 3.3 2.0 - - - -
2736 ALA* 3.3 12.4 + - - +
2746 GLU 3.3 9.0 + - - -
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Residues in contact with VAL 271 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2694 PHE* 3.5 23.3 - - + -
1336 ALA* 3.7 31.0 - - + -
1346 ALA* 4.0 7.4 - - + +
2126 HIS* 4.1 11.7 - - + +
2386 MET* 3.6 37.2 - - + -
2416 ILE* 4.5 8.5 - - + -
2446 MET* 5.5 1.1 - - + -
2636 GLU* 3.5 17.3 + - + +
2706 GLY* 1.3 71.9 - - - -
2726 GLY* 1.3 61.4 + - - +
2746 GLU* 3.4 1.4 + - - -
2756 ILE* 3.2 25.2 + - + +
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Residues in contact with GLY 272 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2616 THR* 3.7 26.2 + - - -
2636 GLU* 2.8 24.2 + - - +
2716 VAL* 1.3 71.5 - - - +
2736 ALA* 1.3 65.8 + - - +
2756 ILE* 3.4 3.8 + - - +
2766 CYS* 3.0 27.4 + - - -
2946 ARG* 3.4 12.1 - - - -
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Residues in contact with ALA 273 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2734 ALA* 3.6 26.8 - - + +
2744 GLU* 3.4 26.2 - - - +
2774 ALA* 4.0 10.8 - - + -
2696 PHE* 4.3 2.9 - - - +
2706 GLY* 3.3 18.5 + - - +
2716 VAL 3.3 0.6 - - - -
2726 GLY* 1.3 77.1 - - - +
2746 GLU* 1.3 61.9 + - - +
2766 CYS* 3.2 2.8 + - - +
2776 ALA* 3.0 19.1 + - - +
2946 ARG* 3.6 11.4 - - - +
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Residues in contact with GLU 274 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2684 GLN* 3.3 13.8 - - + +
2694 PHE* 2.9 55.0 + - + +
2734 ALA* 3.5 3.5 - - - +
2944 ARG* 3.0 36.1 + - - -
2446 MET* 3.6 22.2 - - + -
2706 GLY 3.3 4.8 + - - -
2716 VAL 3.4 0.2 + - - -
2726 GLY 3.3 0.4 - - - -
2736 ALA* 1.3 78.0 - - - +
2756 ILE* 1.3 62.3 + - - +
2766 CYS 3.2 0.2 + - - -
2776 ALA* 3.2 0.7 + - - +
2786 ARG* 3.0 45.6 + - - +
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Residues in contact with ILE 275 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2106 VAL* 3.9 18.2 - - + +
2386 MET* 3.8 31.0 - - + -
2446 MET* 4.0 19.5 - - - -
2466 MET* 3.7 16.8 - - + +
2496 ILE* 4.4 9.4 - - + -
2596 LEU* 4.2 15.0 - - + -
2616 THR* 3.7 28.3 - - + -
2716 VAL* 3.2 16.4 + - + +
2726 GLY 3.7 7.2 - - - +
2746 GLU* 1.3 74.5 - - - +
2766 CYS* 1.3 62.1 + - - +
2786 ARG* 3.4 4.7 + - - -
2796 ILE* 3.1 18.9 + - - +
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Residues in contact with CYS 276 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2764 CYS* 5.5 0.2 - - - -
2774 ALA* 3.8 22.2 - - + -
2804 MET* 3.6 22.6 - - + +
2814 GLU* 6.2 0.7 - - - -
2596 LEU* 5.8 0.2 - - - -
2616 THR* 5.0 5.8 - - - -
2726 GLY 3.0 19.3 + - - -
2736 ALA 3.5 6.7 - - - +
2746 GLU 3.2 0.2 - - - -
2756 ILE* 1.3 71.5 - - - +
2776 ALA* 1.3 68.9 + - - +
2786 ARG 3.0 1.8 - - - -
2796 ILE* 3.2 5.5 + - - +
2806 MET* 3.0 19.2 + - - +
2926 ALA* 4.3 25.6 - - - -
2946 ARG* 4.0 20.0 - - - -
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Residues in contact with ALA 277 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2734 ALA* 3.8 16.5 + - + +
2764 CYS* 4.2 15.0 - - + -
2944 ARG* 3.5 35.2 - - - +
2736 ALA 3.0 13.6 + - - +
2746 GLU 3.7 2.7 - - - +
2766 CYS* 1.3 79.4 - - - +
2786 ARG* 1.3 58.1 + - - +
2806 MET* 3.6 3.2 + - - +
2816 GLU* 2.9 36.3 + - - +
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Residues in contact with ARG 278 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2684 GLN* 3.8 18.2 + - - +
2944 ARG* 4.3 6.7 - - - +
3495 ARG* 5.4 4.0 - - - +
2446 MET* 4.6 17.7 + - - +
2466 MET* 3.7 44.4 - - + +
2506 GLU* 3.9 3.1 + - - +
2746 GLU* 3.0 43.4 + - + +
2756 ILE* 3.7 5.4 - - - +
2766 CYS 3.0 0.8 - - - -
2776 ALA* 1.3 76.0 - - - +
2796 ILE* 1.3 66.4 + - - +
2816 GLU* 3.2 8.0 + - - +
2826 GLY* 2.8 24.6 + - - -
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Residues in contact with ILE 279 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2804 MET* 5.3 3.1 - - + -
2466 MET* 3.7 20.2 - - + -
2496 ILE* 4.5 1.8 - - + -
2506 GLU* 4.3 7.2 - - + -
2536 VAL* 4.4 11.4 - - + -
2596 LEU* 3.3 32.1 - - + -
2756 ILE 3.1 9.7 + - - +
2766 CYS* 3.2 8.7 + - - +
2786 ARG* 1.3 77.0 - - - +
2806 MET* 1.3 65.2 - - - +
2826 GLY* 3.1 8.5 + - - -
2846 ALA* 3.8 22.8 + - + -
2856 PHE* 3.6 18.9 + - - +
2886 LEU* 3.7 34.8 - - + -
2926 ALA* 5.4 2.2 - - + -
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Residues in contact with MET 280 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2764 CYS* 3.6 52.0 - - + +
2794 ILE* 4.6 4.9 - - + -
2804 MET* 4.0 18.2 - - + -
2854 PHE* 4.9 4.0 - - - -
2884 LEU* 4.4 13.7 - - - -
2914 PRO* 3.5 31.1 - - + +
2924 ALA* 3.8 28.0 - - + +
2766 CYS 3.0 14.5 + - - +
2776 ALA 3.9 2.9 - - - +
2796 ILE* 1.3 78.1 - - - +
2816 GLU* 1.3 60.8 + - - +
2826 GLY 3.4 1.6 + - - +
2856 PHE* 3.5 34.2 - - + +
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Residues in contact with GLU 281 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2764 CYS* 5.8 0.7 - - - -
2914 PRO* 5.3 2.2 - - - -
2924 ALA 3.9 18.6 - - - +
2934 VAL* 4.4 2.0 - - + -
2944 ARG* 3.0 56.4 + - + -
3495 ARG* 3.3 23.2 + - - -
3535 GLN* 2.9 45.7 + - + +
2776 ALA* 2.9 19.7 + - - +
2786 ARG* 4.0 8.9 - - - +
2806 MET* 1.3 75.4 - - + +
2826 GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 282 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2506 GLU* 3.8 5.6 - - - -
2786 ARG 2.8 16.8 + - - -
2796 ILE 3.1 4.8 + - - -
2806 MET 3.9 5.5 - - - +
2816 GLU* 1.3 82.2 - - - +
2836 PRO* 1.3 70.8 - - - +
2846 ALA 3.2 5.7 + - - -
2856 PHE* 4.0 5.5 + - - +
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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