Contacts of the helix formed by residues 270 - 282 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1344 ALA* 3.8 11.4 - - - -
2634 GLU* 3.7 1.3 - - - -
2664 TRP 3.9 13.2 - - - -
2674 PRO 3.3 11.7 + - - -
2684 GLN 3.0 3.8 - - - -
2694 PHE* 1.3 80.2 - - - +
2714 VAL* 1.3 67.4 + - - +
2724 GLY 3.3 2.7 - - - -
2734 ALA* 3.0 17.4 + - - +
2744 GLU 3.5 2.8 + - - -
1386 HIS* 4.0 3.6 - - - -
2696 PHE* 4.0 4.6 - - - -
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Residues in contact with VAL 271 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1314 CYS* 6.2 0.2 - - - -
1334 ALA* 4.0 27.1 - - + -
1344 ALA* 4.0 11.0 - - + +
2124 HIS* 4.4 8.3 - - + +
2384 MET* 4.0 22.2 - - + -
2414 ILE* 4.7 5.8 - - + -
2444 MET* 4.0 25.4 - - + -
2634 GLU* 2.8 25.2 + - + +
2704 GLY* 1.3 70.4 - - - -
2724 GLY* 1.3 59.9 + - - +
2744 GLU* 2.9 13.3 + - - +
2754 ILE* 3.1 15.9 + - + +
2696 PHE* 3.7 16.6 - - + -
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Residues in contact with GLY 272 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2614 THR* 3.7 28.7 - - - +
2634 GLU* 2.5 25.0 + - - -
2714 VAL* 1.3 72.2 - - - +
2734 ALA* 1.3 62.4 + - - +
2754 ILE* 3.3 3.1 + - - +
2764 CYS* 3.0 28.4 + - - -
2944 ARG* 3.5 10.5 - - - -
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Residues in contact with ALA 273 (chain 4).
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* 4.2 3.4 - - - +
2704 GLY 3.0 22.1 + - - +
2724 GLY* 1.3 76.2 - - - +
2744 GLU* 1.3 54.0 + - - +
2764 CYS* 3.4 3.5 - - - +
2774 ALA* 3.1 22.2 + - - +
2944 ARG* 3.4 26.9 - - - +
2696 PHE* 5.9 0.2 - - - -
2736 ALA* 3.6 26.4 - - + +
2746 GLU* 3.5 16.8 - - - +
2776 ALA* 3.8 7.4 - - + -
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Residues in contact with GLU 274 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2444 MET* 4.4 5.8 - - - -
2704 GLY 3.5 1.2 + - - -
2714 VAL 2.9 5.7 + - - +
2734 ALA* 1.3 74.1 - - - +
2754 ILE* 1.3 66.5 - - - +
2764 CYS 2.9 1.9 + - - -
2774 ALA* 2.9 1.4 + - - -
2784 ARG* 2.8 56.2 + - + +
2676 PRO 4.9 0.3 - - - -
2686 GLN* 3.6 21.2 - - - +
2696 PHE* 3.2 54.8 + - + +
2736 ALA* 3.4 5.1 - - - +
2946 ARG* 3.1 29.0 + - - -
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Residues in contact with ILE 275 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104 VAL* 3.7 26.2 - - + -
2384 MET* 3.9 16.6 - - + -
2444 MET* 3.8 21.8 - - + -
2464 MET* 3.6 16.6 - - + +
2494 ILE* 4.1 20.4 - - + -
2594 LEU* 4.5 6.3 - - + -
2614 THR* 3.8 30.7 - - + -
2714 VAL* 3.1 18.7 + - + +
2724 GLY* 4.0 1.6 - - - +
2744 GLU* 1.3 75.8 - - - +
2764 CYS* 1.3 56.3 + - - +
2784 ARG* 4.0 5.4 - - - -
2794 ILE* 3.1 25.5 + - - +
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Residues in contact with CYS 276 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2594 LEU* 5.5 1.8 - - - -
2614 THR* 5.0 7.0 - - - -
2724 GLY 3.0 17.2 + - - +
2734 ALA 3.4 10.5 - - - +
2744 GLU 2.9 0.8 - - - -
2754 ILE* 1.3 76.7 - - - +
2774 ALA* 1.3 66.9 + - - +
2784 ARG 3.2 0.2 - - - -
2794 ILE* 3.4 6.4 + - - +
2804 MET* 3.1 22.7 + - - +
2924 ALA* 4.4 16.8 - - - -
2934 VAL 5.5 0.4 - - - -
2944 ARG* 4.0 22.0 - - - -
2776 ALA* 4.2 14.6 - - + -
2806 MET* 3.6 27.8 - - + +
2816 GLU* 5.8 0.2 - - - -
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Residues in contact with ALA 277 (chain 4).
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 3.1 9.9 + - - +
2744 GLU 2.9 5.7 + - - +
2764 CYS* 1.3 78.4 - - - +
2784 ARG* 1.3 64.3 + - - +
2804 MET* 3.1 8.1 + - - +
2814 GLU* 2.9 28.4 + - - +
2736 ALA* 4.0 7.4 - - + -
2766 CYS* 3.8 26.2 - - + -
2946 ARG* 3.5 31.9 - - - +
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Residues in contact with ARG 278 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3493 ARG* 4.8 3.8 - - - +
2444 MET* 4.3 16.7 + - - +
2464 MET* 3.4 52.8 - - + +
2504 GLU* 4.8 1.1 - - - -
2744 GLU* 2.8 38.6 + - + +
2754 ILE* 3.7 0.9 - - - +
2774 ALA* 1.3 76.0 - - - +
2794 ILE* 1.3 65.6 + - - +
2814 GLU* 3.0 21.3 + - - +
2824 GLY* 2.8 23.3 + - - -
2686 GLN* 3.1 27.9 + - - +
2946 ARG* 4.0 2.0 - - - +
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Residues in contact with ILE 279 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2464 MET* 3.5 21.6 - - + +
2494 ILE* 4.6 2.5 - - + -
2504 GLU* 4.1 12.6 - - + +
2534 VAL* 4.5 14.4 - - + -
2594 LEU* 3.5 29.2 - - + -
2754 ILE 3.1 11.5 + - - +
2764 CYS* 3.6 7.2 - - - +
2784 ARG* 1.3 78.2 - - - +
2804 MET* 1.3 63.4 + - - +
2824 GLY* 3.3 15.6 + - - +
2844 ALA* 3.9 25.1 - - + -
2854 PHE* 3.6 14.1 + - + +
2884 LEU* 3.9 28.3 - - + -
2806 MET* 4.6 6.5 - - + -
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Residues in contact with MET 280 (chain 4).
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 3.1 5.9 + - - +
2774 ALA* 3.1 9.7 + - - +
2784 ARG 3.0 0.2 + - - -
2794 ILE* 1.3 80.7 - - + +
2814 GLU* 1.3 61.2 + - - +
2824 GLY 3.7 0.7 - - - +
2854 PHE* 3.4 38.8 - - + +
2766 CYS* 3.6 39.5 - - + +
2796 ILE* 5.3 0.9 - - + -
2806 MET* 4.0 28.5 - - + +
2856 PHE* 5.0 0.7 - - - -
2886 LEU* 4.5 12.6 - - + -
2916 PRO* 3.3 20.6 - - + +
2926 ALA* 3.7 40.6 - - + +
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Residues in contact with GLU 281 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3493 ARG* 2.5 49.4 + - - -
3533 GLN* 3.1 37.9 + - + +
2774 ALA* 2.9 23.0 + - - +
2784 ARG* 3.9 12.5 - - - +
2804 MET* 1.3 70.1 - - + +
2824 GLY* 1.3 67.4 + - - +
2766 CYS* 6.2 1.3 - - - -
2916 PRO* 4.9 4.6 - - - +
2926 ALA 4.4 13.9 - - - +
2936 VAL* 5.0 1.6 - - - -
2946 ARG* 3.1 30.9 + - - +
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Residues in contact with GLY 282 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2504 GLU* 3.6 11.2 - - - -
2784 ARG 2.8 11.4 + - - -
2794 ILE 3.3 7.0 + - - +
2804 MET 3.3 4.8 - - - +
2814 GLU* 1.3 82.7 - - - +
2834 PRO* 1.3 76.2 - - - +
2844 ALA 3.3 2.8 + - - -
2854 PHE* 3.6 5.9 + - - +
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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