Contacts of the helix formed by residues 3715 - 3731 (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 ASP3715 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2119B ARG* 5.9 0.9 - - - +
3701B PHE* 6.0 0.7 - - + -
3713B ASP* 4.6 7.8 - - + +
3714B GLU* 1.3 82.7 - - - +
3716B TYR* 1.3 63.2 + - - +
3717B LEU* 3.1 17.3 - - + -
3718B TYR* 2.9 35.5 + - + +
3719B MET* 3.6 5.7 + - - +
3788B MET* 4.0 13.0 - - - +
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Residues in contact with TYR3716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2123B SER* 4.8 14.5 - - - -
2126B HIS* 6.2 4.5 - + - -
2127B ARG* 5.9 4.8 - - + -
3714B GLU* 3.5 16.3 - - + +
3715B ASP* 1.3 77.4 - - - +
3717B LEU* 1.3 76.2 + - + +
3718B TYR 3.2 0.2 - - - -
3719B MET* 3.7 6.6 + - - +
3720B ALA* 3.3 23.1 + - + +
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Residues in contact with LEU3717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2119B ARG* 3.5 56.1 - - + +
2122B PHE* 5.6 4.7 - - + -
2123B SER* 5.3 12.1 - - - +
2126B HIS* 6.2 0.4 - - - -
3700B HIS* 4.5 10.1 - - + +
3701B PHE* 4.2 17.9 - - + -
3715B ASP* 3.1 21.2 - - + -
3716B TYR* 1.3 97.9 - - + +
3718B TYR* 1.3 72.2 + - - +
3720B ALA* 3.5 5.7 + - - -
3721B TYR* 3.4 35.2 + - + +
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Residues in contact with TYR3718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3701B PHE* 3.5 51.3 - + + +
3715B ASP* 2.9 21.1 + - + +
3717B LEU* 1.3 81.7 - - - +
3719B MET* 1.3 59.0 + - - +
3720B ALA 3.2 0.2 + - - -
3721B TYR* 3.5 1.8 + - + +
3722B ALA* 3.0 33.1 + - + +
3773B MET* 4.4 14.9 + - - +
3774B VAL* 5.3 2.9 - - - +
3777B MET* 3.8 26.9 - - + +
3788B MET* 3.7 25.4 - - + -
3791B SER* 6.5 0.2 - - - -
3792B THR* 3.4 33.3 - - + +
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Residues in contact with MET3719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3714B GLU 6.1 0.2 - - - +
3715B ASP 3.6 6.8 + - - +
3716B TYR* 3.7 7.8 + - - +
3718B TYR* 1.3 78.9 - - - +
3720B ALA* 1.3 62.4 + - - +
3722B ALA* 3.8 8.6 - - - +
3723B ASP* 3.6 19.1 + - - +
3787B ALA 6.1 0.4 - - - -
3788B MET* 5.7 7.3 - - + +
3791B SER* 4.0 21.3 - - - +
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Residues in contact with ALA3720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2126B HIS* 3.4 37.4 - - + +
3716B TYR* 3.3 18.2 + - + +
3717B LEU* 3.7 9.9 - - - +
3718B TYR 3.1 1.0 - - - -
3719B MET* 1.3 80.8 - - - +
3721B TYR* 1.3 63.6 + - + +
3723B ASP* 3.7 2.3 + - - +
3724B ILE* 3.3 26.8 + - - +
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Residues in contact with TYR3721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122B PHE* 2.3 51.8 + + + -
2123B SER* 4.9 1.6 - - - -
2125B LEU* 3.3 19.9 - - + +
2126B HIS* 3.3 29.0 + + + -
3673B LEU* 5.4 3.6 - - + -
3697B LEU* 4.3 22.7 - - + -
3701B PHE* 5.2 15.7 - + + -
3717B LEU* 3.4 25.1 + - + +
3718B TYR* 4.4 2.0 - - + +
3720B ALA* 1.3 80.1 - - + +
3722B ALA* 1.3 59.8 + - - +
3724B ILE* 3.8 16.8 - - + +
3725B MET* 2.9 43.8 + - + +
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Residues in contact with ALA3722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3718B TYR* 3.0 29.4 + - + +
3719B MET* 3.9 10.3 - - - +
3720B ALA 3.2 0.4 - - - -
3721B TYR* 1.3 77.8 - - - +
3723B ASP* 1.3 57.8 + - - +
3726B ALA* 3.0 32.4 + - - +
3791B SER* 4.3 26.5 - - - +
3792B THR* 5.8 1.1 - - + -
3795B LEU* 3.5 16.7 - - + +
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Residues in contact with ASP3723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3719B MET 3.6 12.8 + - - +
3720B ALA 4.3 2.7 - - - +
3721B TYR 3.4 0.2 - - - -
3722B ALA* 1.3 79.6 - - - +
3724B ILE* 1.3 64.2 + - + +
3726B ALA* 4.4 3.1 - - - +
3727B LYS* 3.2 26.0 + - - +
3794B LYS* 6.2 3.4 - - - -
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Residues in contact with ILE3724 (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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2126B HIS* 3.7 23.8 - - + +
3665B PHE* 3.6 29.8 - - + -
3666B GLU* 3.2 41.3 - - + +
3669B MET* 4.4 15.0 - - + -
3670B ILE* 4.7 7.8 - - + +
3720B ALA 3.3 20.6 + - - +
3721B TYR* 3.5 16.8 + - + +
3722B ALA 3.3 0.8 - - - -
3723B ASP* 1.3 78.3 - - + +
3725B MET* 1.3 59.3 + - - +
3728B SER* 3.0 16.5 + - - -
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Residues in contact with MET3725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670B ILE* 4.4 18.2 - - + -
3694B LEU* 5.8 6.7 - - + -
3697B LEU* 5.1 20.4 - - + -
3698B VAL* 6.1 0.9 - - - +
3701B PHE* 6.3 2.5 - - + -
3721B TYR* 2.9 28.3 + - + +
3724B ILE* 1.3 78.5 - - - +
3726B ALA* 1.3 60.2 + - - +
3728B SER* 2.7 19.2 + - - +
3729B CYS* 3.5 11.3 + - - +
3765B LEU* 3.6 42.3 - - + +
3770B ALA* 5.2 7.2 - - - -
3795B LEU* 3.8 21.3 - - + -
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Residues in contact with ALA3726 (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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3722B ALA 3.0 19.1 + - - +
3723B ASP* 4.4 3.8 - - - +
3725B MET* 1.3 75.1 - - - +
3727B LYS* 1.3 65.5 + - - +
3729B CYS* 3.4 1.3 + - - -
3730B HIS* 3.3 13.2 + - - +
3794B LYS* 4.2 15.3 - - + +
3795B LEU* 3.8 32.0 - - + +
3798B SER* 3.2 26.2 + - - -
3799B ILE* 6.5 0.2 - - - -
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Residues in contact with LYS3727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3666B GLU* 3.9 16.2 - - + -
3723B ASP 3.2 20.0 + - - +
3726B ALA* 1.3 77.5 - - - +
3728B SER* 1.3 57.6 + - - +
3730B HIS* 4.8 2.5 - - - +
3731B LEU* 2.9 35.7 + - + +
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Residues in contact with SER3728 (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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3666B GLU* 3.2 31.1 - - - +
3667B ASP* 4.5 8.1 - - - +
3670B ILE* 3.6 16.2 - - - +
3724B ILE 3.0 9.1 + - - -
3725B MET* 2.7 26.7 + - - +
3727B LYS* 1.3 77.7 - - - +
3729B CYS* 1.3 60.6 + - - +
3731B LEU 3.8 12.9 - - - -
3761B GLN* 3.5 16.3 - - - +
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Residues in contact with CYS3729 (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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3725B MET 3.5 8.5 + - - +
3726B ALA* 3.4 3.0 + - - +
3727B LYS 3.3 0.2 - - - -
3728B SER* 1.3 82.1 + - - +
3730B HIS* 1.3 61.4 + - - +
3731B LEU 4.9 0.3 - - - +
3758B LEU* 4.6 12.6 - - - +
3761B GLN* 3.4 28.2 - - - +
3762B GLN* 4.0 25.1 - - - -
3765B LEU* 4.7 4.5 - - + -
3798B SER* 3.2 36.1 - - - +
3799B ILE* 3.9 19.7 - - + -
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Residues in contact with HIS3730 (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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3726B ALA 3.3 12.7 + - - +
3727B LYS* 4.4 2.9 - - - +
3729B CYS* 1.3 82.9 - - - +
3731B LEU* 1.3 61.9 + - + +
3758B LEU* 5.2 11.8 - - - +
3798B SER* 4.2 12.6 - - - +
3801B ASN* 5.0 15.0 - - - +
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Residues in contact with LEU3731 (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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3667B ASP* 6.0 3.4 - - - -
3727B LYS* 2.9 22.2 + - + +
3728B SER* 3.8 14.0 - - - +
3729B CYS 4.9 0.7 - - - +
3730B HIS* 1.3 80.8 - - + +
3761B GLN* 5.2 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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