Contacts of the helix formed by residues 3665 - 3674 (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 PHE3665 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2126B HIS* 4.9 2.5 - + - -
2129B TYR* 3.5 38.4 + + + +
2130B ASP* 3.5 33.4 - - + -
2132B LEU* 5.9 7.2 - - + -
2133B GLY 6.0 1.6 - - - -
3663B HIS* 3.4 28.9 - - + -
3664B SER* 1.3 74.7 - - - +
3666B GLU* 1.3 62.3 + - - +
3667B ASP* 3.2 3.8 + - - -
3668B ARG* 3.8 5.1 + - - +
3669B MET* 3.4 20.6 + - + +
3724B ILE* 3.6 32.8 - - + -
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Residues in contact with GLU3666 (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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3664B SER* 3.1 6.6 - - - +
3665B PHE* 1.3 79.3 - - - +
3667B ASP* 1.3 62.2 + - - +
3670B ILE* 3.4 13.3 + - - +
3724B ILE* 3.2 39.3 - - + +
3727B LYS* 3.9 21.1 - - + -
3728B SER* 3.2 21.5 - - - +
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Residues in contact with ASP3667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3664B SER 4.3 5.6 + - - +
3665B PHE 3.2 1.2 - - - -
3666B GLU* 1.3 78.3 - - - +
3668B ARG* 1.3 64.7 + - - +
3669B MET 3.1 1.2 + - - -
3670B ILE* 3.3 11.3 + - - +
3671B ASP* 2.7 32.2 + - - +
3728B SER* 4.5 10.4 - - - +
3731B LEU 6.0 3.6 - - - -
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Residues in contact with ARG3668 (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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2129B TYR* 3.4 21.6 + - - +
3665B PHE* 3.8 5.5 + - - +
3666B GLU 3.7 0.2 - - - -
3667B ASP* 1.3 82.4 - - - +
3669B MET* 1.3 60.7 + - - +
3670B ILE 3.3 0.4 - - - -
3671B ASP* 3.8 9.5 - - - +
3672B ASP* 3.6 23.4 + - - +
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Residues in contact with MET3669 (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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2125B LEU* 6.0 4.1 - - + +
2129B TYR* 3.6 25.5 + - + -
3665B PHE* 3.4 20.2 + - + +
3666B GLU 4.4 3.4 - - - +
3667B ASP 3.1 1.2 + - - -
3668B ARG* 1.3 78.5 - - - +
3670B ILE* 1.3 62.8 - - + +
3672B ASP* 4.5 1.6 - - - +
3673B LEU* 3.4 24.4 + - - +
3724B ILE* 4.4 16.2 - - + -
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Residues in contact with ILE3670 (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 3.4 19.1 - - - +
3667B ASP 3.3 5.2 + - - +
3669B MET* 1.3 82.3 - - + +
3671B ASP* 1.3 67.1 + - - +
3673B LEU* 3.5 6.6 + - + +
3674B SER* 3.1 22.0 + - - -
3694B LEU* 3.9 22.8 - - + +
3721B TYR* 6.3 3.4 - - + -
3724B ILE* 4.7 8.5 - - + +
3725B MET* 4.4 26.0 - - + -
3728B SER* 3.6 21.1 - - - +
3764B ARG* 3.6 29.2 - - - +
3765B LEU* 5.5 4.3 - - + -
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Residues in contact with ASP3671 (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* 2.7 38.0 + - - +
3668B ARG* 3.8 7.4 + - - +
3669B MET 3.6 0.2 - - - -
3670B ILE* 1.3 78.2 - - - +
3672B ASP* 1.3 57.5 + - - +
3674B SER 3.1 3.5 + - - -
3675B LYS* 2.9 29.9 + - - +
3764B ARG* 3.5 33.6 + - - +
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Residues in contact with ASP3672 (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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2104B VAL* 4.6 13.4 - - + +
3668B ARG 3.6 16.2 + - - +
3669B MET* 5.0 1.1 - - - +
3670B ILE 3.4 0.4 - - - -
3671B ASP* 1.3 79.1 - - - +
3673B LEU* 1.3 61.7 + - - +
3675B LYS* 3.6 16.7 + - - +
3676B ALA 4.9 0.7 + - - -
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Residues in contact with LEU3673 (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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2104B VAL* 4.1 24.0 - - + +
2107B ALA* 5.6 4.3 - - + -
2122B PHE* 5.3 9.2 - - + -
2125B LEU* 4.4 27.1 - - + -
3669B MET 3.4 19.7 + - - +
3670B ILE* 3.5 7.5 + - + +
3671B ASP 3.2 0.6 - - - -
3672B ASP* 1.3 78.5 - - - +
3674B SER* 1.3 58.1 + - - +
3675B LYS 3.5 0.4 - - - -
3676B ALA 5.2 0.2 + - - -
3693B PRO* 3.2 40.1 - - + +
3694B LEU* 3.8 24.5 + - + -
3697B LEU* 3.9 25.4 - - + -
3721B TYR* 5.4 3.4 - - + -
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Residues in contact with SER3674 (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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3670B ILE 3.1 16.8 + - - -
3671B ASP 3.1 3.6 + - - -
3673B LEU* 1.3 75.7 - - - +
3675B LYS* 1.3 65.0 + - - +
3676B ALA* 3.6 4.1 - - - -
3692B ASP* 5.2 5.9 - - - +
3693B PRO* 5.2 2.9 - - - -
3694B LEU* 3.6 36.5 + - - +
3764B ARG* 4.9 13.2 + - - +
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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