Contacts of the helix formed by residues 2798 - 2819 (chain B) in PDB entry 6X34
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 SER2798 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2796B THR 3.9 1.4 + - - -
2797B PHE* 1.3 77.8 - - - +
2799B GLU* 1.3 63.7 + - - +
2800B LYS* 3.3 8.1 - - - -
2801B ASP* 3.9 8.9 - - - +
2802B LYS* 3.0 27.0 + - - +
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Residues in contact with GLU2799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2798B SER* 1.3 76.9 - - - +
2800B LYS* 1.3 61.5 + - - +
2802B LYS* 4.0 5.0 - - - +
2803B GLU* 3.2 24.3 + - - +
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Residues in contact with LYS2800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2798B SER* 3.3 4.9 - - - -
2799B GLU* 1.3 77.2 - - - +
2801B ASP* 1.3 64.1 + - - +
2803B GLU* 3.5 13.8 + - - +
2804B ILE* 3.8 9.5 + - - +
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Residues in contact with ASP2801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2797B PHE* 3.8 23.8 - - + -
2798B SER* 3.5 10.6 + - - +
2799B GLU 3.4 0.2 - - - -
2800B LYS* 1.3 78.5 - - - +
2802B LYS* 1.3 62.2 + - - +
2804B ILE* 3.4 18.3 + - - +
2805B TYR* 4.4 2.8 + - - +
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Residues in contact with LYS2802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2759B ALA* 4.9 5.0 - - + +
2794B TYR 5.7 2.2 - - - +
2797B PHE* 4.4 9.1 - - + +
2798B SER 3.0 19.2 + - - +
2799B GLU* 4.1 5.4 - - - +
2801B ASP* 1.3 76.5 - - - +
2803B GLU* 1.3 57.4 + - - +
2804B ILE 3.2 0.6 + - - -
2805B TYR* 3.5 5.3 + - - +
2806B ARG* 3.2 28.0 + - + +
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Residues in contact with GLU2803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2799B GLU 3.2 18.9 + - - +
2800B LYS* 3.8 7.9 - - - +
2801B ASP 3.3 0.6 - - - -
2802B LYS* 1.3 74.8 - - - +
2804B ILE* 1.3 63.7 + - - +
2805B TYR 3.3 0.4 - - - -
2806B ARG* 3.8 9.0 - - - -
2807B TRP* 3.2 26.0 + - - +
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Residues in contact with ILE2804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2800B LYS 3.8 6.8 + - - +
2801B ASP* 3.4 14.2 + - - +
2802B LYS 3.2 0.8 - - - -
2803B GLU* 1.3 79.9 - - - +
2805B TYR* 1.3 60.2 + - + +
2807B TRP* 4.2 8.6 + - - +
2808B PRO* 4.6 5.0 - - - +
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Residues in contact with TYR2805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2759B ALA* 4.1 31.3 - - + +
2762B THR* 5.1 9.4 - - - -
2763B HIS* 5.2 7.9 - - + +
2801B ASP 4.4 2.6 + - - +
2802B LYS* 3.5 6.0 + - - +
2804B ILE* 1.3 77.5 - - + +
2806B ARG* 1.3 64.0 + - - +
2807B TRP 3.3 0.8 + - - -
2808B PRO* 3.8 12.6 - - - +
2809B ILE* 3.8 10.7 + - - +
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Residues in contact with ARG2806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2755B ILE* 5.3 10.7 - - + +
2756B ASN* 6.5 0.2 - - - -
2759B ALA* 4.3 12.7 - - + +
2802B LYS* 3.2 19.2 + - + +
2803B GLU* 4.2 6.3 - - - -
2804B ILE 3.5 0.2 - - - -
2805B TYR* 1.3 76.4 - - - +
2807B TRP* 1.3 59.7 + - - +
2808B PRO 3.3 0.2 - - - -
2809B ILE* 3.9 5.1 - - - +
2810B LYS* 3.0 32.1 + - - +
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Residues in contact with TRP2807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2803B GLU 3.2 19.8 + - - +
2804B ILE* 4.3 6.1 - - - +
2805B TYR 3.3 0.4 - - - -
2806B ARG* 1.3 78.1 - - - +
2808B PRO* 1.3 56.9 - - - +
2810B LYS* 4.0 4.4 - - - +
2811B GLU* 3.0 30.1 + - - +
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Residues in contact with PRO2808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2804B ILE 4.6 4.7 - - - +
2805B TYR* 3.8 10.8 - - - +
2806B ARG 3.3 0.4 - - - -
2807B TRP* 1.3 80.6 - - - +
2809B ILE* 1.3 60.9 + - - +
2811B GLU* 3.7 4.5 + - + +
2812B SER* 3.3 22.9 + - - -
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Residues in contact with ILE2809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2755B ILE* 4.9 14.8 - - + +
2758B PHE* 4.7 20.4 - - + -
2759B ALA* 5.5 1.1 - - - +
2805B TYR 3.8 9.8 + - - +
2806B ARG* 3.5 8.0 + - - +
2807B TRP 3.3 0.4 - - - -
2808B PRO* 1.3 76.9 - - - +
2810B LYS* 1.3 61.8 + - - +
2812B SER* 3.5 5.0 + - - -
2813B LEU* 3.0 28.9 + - - +
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Residues in contact with LYS2810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2755B ILE* 5.9 5.3 - - + +
2806B ARG 3.0 18.8 + - - +
2807B TRP* 4.0 4.9 - - - +
2808B PRO 3.4 0.2 - - - -
2809B ILE* 1.3 76.5 - - - +
2811B GLU* 1.3 59.8 + - - +
2813B LEU* 3.9 5.1 - - - +
2814B LYS* 2.9 31.9 + - - +
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Residues in contact with GLU2811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2742B THR* 4.8 8.7 - - - -
2807B TRP 3.0 18.3 + - - +
2808B PRO* 4.0 5.4 - - + +
2809B ILE 3.3 0.2 - - - -
2810B LYS* 1.3 78.5 - - - +
2812B SER* 1.3 60.2 + - - +
2814B LYS* 3.6 6.0 + - - +
2815B ALA* 3.2 22.9 + - - +
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Residues in contact with SER2812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2808B PRO 3.3 16.1 + - - -
2809B ILE* 3.9 5.6 - - - -
2811B GLU* 1.3 77.2 - - - +
2813B LEU* 1.3 63.8 + - - +
2815B ALA* 3.5 7.3 + - - +
2816B MET* 3.4 20.1 + - - +
2878B LEU* 6.3 2.7 - - - -
2926B LEU* 5.4 12.1 - - - -
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Residues in contact with LEU2813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2751B LEU* 6.3 3.8 - - + -
2809B ILE 3.0 18.2 + - - +
2810B LYS* 3.9 5.2 - - - +
2812B SER* 1.3 75.4 - - - +
2814B LYS* 1.3 63.5 + - - +
2816B MET* 3.4 7.1 + - - +
2817B ILE* 3.2 21.7 + - - +
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Residues in contact with LYS2814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2742B THR* 3.8 23.0 - - - +
2745B VAL* 3.8 31.0 - - + +
2810B LYS 2.9 18.8 + - - +
2811B GLU* 4.0 2.2 - - - +
2812B SER 3.3 0.2 - - - -
2813B LEU* 1.3 75.1 - - - +
2815B ALA* 1.3 63.9 + - - +
2817B ILE* 3.4 6.5 + - - +
2818B ALA* 3.3 20.6 + - - +
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Residues in contact with ALA2815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2740B VAL* 4.8 19.3 - - + +
2741B GLU 6.0 0.4 - - - -
2742B THR* 4.8 5.8 - - - +
2811B GLU 3.2 17.2 + - - +
2812B SER* 3.8 7.6 - - - +
2813B LEU 3.3 0.2 - - - -
2814B LYS* 1.3 77.1 - - - +
2816B MET* 1.3 60.5 + - - +
2818B ALA* 3.4 14.7 + - - +
2819B TRP* 3.5 12.1 + - - +
2881B ASN* 5.2 13.9 - - + -
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Residues in contact with MET2816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2812B SER 3.4 11.0 + - - +
2813B LEU* 3.4 8.5 + - - +
2814B LYS 3.3 0.4 - - - -
2815B ALA* 1.3 76.5 - - - +
2817B ILE* 1.3 64.7 + - - +
2819B TRP* 3.3 14.3 + - - +
2821B TRP* 3.3 32.3 + - + +
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Residues in contact with ILE2817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2745B VAL* 5.2 6.7 - - + -
2746B ILE 5.3 7.4 - - - +
2813B LEU 3.2 16.1 + - - +
2814B LYS* 3.7 8.5 - - - +
2815B ALA 3.3 0.6 - - - -
2816B MET* 1.3 78.7 - - - +
2818B ALA* 1.3 60.7 + - - +
2820B GLU* 3.4 12.0 + - - -
2821B TRP 4.5 6.8 + - - +
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Residues in contact with ALA2818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2740B VAL* 5.2 9.4 - - + -
2741B GLU 4.5 15.0 - - - +
2745B VAL* 5.7 3.1 - - + +
2814B LYS 3.3 10.7 + - - +
2815B ALA* 3.8 11.2 - - - +
2816B MET 3.3 0.8 - - - -
2817B ILE* 1.3 79.0 - - - +
2819B TRP* 1.3 55.5 + - - +
2820B GLU* 3.2 5.3 + - - +
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Residues in contact with TRP2819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2815B ALA 3.5 10.0 + - - +
2816B MET* 3.3 12.0 + - - +
2817B ILE 3.2 1.0 - - - -
2818B ALA* 1.3 76.9 - - - +
2820B GLU* 1.3 68.1 + - - +
2821B TRP* 3.3 5.4 + - + +
2939B ARG* 5.4 4.7 - - - +
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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