Contacts of the helix formed by residues 3641 - 3658 (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 PRO3641 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3639B ASN 4.5 2.2 - - - +
3640B LEU* 1.3 85.6 - - + +
3642B THR* 1.3 65.8 + - - +
3643B HIS* 3.1 6.9 + - + +
3644B ARG* 4.0 13.4 - - + +
3645B ALA* 3.1 23.4 + - - +
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Residues in contact with THR3642 (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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1967B VAL* 5.4 5.2 - - - +
1968B ASP* 5.7 6.1 - - - +
1971B GLN* 4.4 16.2 + - - -
3640B LEU 3.1 6.8 + - - -
3641B PRO* 1.3 69.0 - - - +
3643B HIS* 1.3 67.0 + - + +
3645B ALA* 3.8 7.6 - - - +
3646B CYS* 3.3 22.7 + - - +
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Residues in contact with HIS3643 (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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2144B THR* 3.8 19.2 - - - +
2145B ILE 4.5 4.7 - - - -
2146B SER* 4.0 34.8 - - - +
2195B HIS* 4.7 10.5 - - + -
3641B PRO* 3.1 4.6 - - + +
3642B THR* 1.3 85.2 - - + +
3644B ARG* 1.3 62.0 + - - +
3646B CYS* 3.7 8.7 + - - +
3647B ASN* 3.8 5.7 + - - +
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Residues in contact with ARG3644 (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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2143B TYR* 5.1 9.9 - - - +
2195B HIS* 5.1 7.8 - - + +
3641B PRO* 3.5 15.5 + - + +
3643B HIS* 1.3 77.0 - - - +
3645B ALA* 1.3 63.9 + - - +
3646B CYS 3.3 0.2 - - - -
3647B ASN* 3.5 8.2 + - - +
3648B MET* 3.3 19.6 + - - +
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Residues in contact with ALA3645 (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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1967B VAL* 3.8 22.6 - - + +
1971B GLN* 5.3 5.4 - - - +
2007B ILE* 5.5 5.6 - - + +
3637B LEU* 5.0 13.2 - - + -
3640B LEU* 5.3 6.1 - - + -
3641B PRO 3.1 19.3 + - - +
3642B THR* 4.1 9.2 - - - +
3643B HIS 3.3 0.4 - - - -
3644B ARG* 1.3 76.7 - - - +
3646B CYS* 1.3 63.2 + - - +
3648B MET* 3.3 19.1 + - - +
3649B PHE 3.7 3.8 + - - -
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Residues in contact with CYS3646 (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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1963B ALA* 4.9 6.1 - - + +
1964B GLU* 4.4 15.7 - - + +
1967B VAL* 3.8 24.6 - - + +
2144B THR* 4.3 20.3 + - + +
3642B THR* 3.3 16.3 + - - +
3643B HIS* 4.1 4.7 - - - +
3644B ARG 3.3 0.2 - - - -
3645B ALA* 1.3 78.9 - - - +
3647B ASN* 1.3 61.7 + - - +
3649B PHE* 3.3 17.3 + - - +
3650B LEU* 4.1 6.6 + - - +
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Residues in contact with ASN3647 (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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2143B TYR* 3.8 35.7 - - + +
2144B THR* 4.2 22.8 - - - +
3643B HIS 3.8 4.0 + - - +
3644B ARG* 3.5 9.3 + - - +
3645B ALA 3.3 0.6 - - - -
3646B CYS* 1.3 77.6 - - - +
3648B MET* 1.3 63.3 + - - +
3649B PHE 3.2 0.4 - - - -
3650B LEU* 3.3 23.7 + - + +
3651B GLU* 4.0 4.0 + - - +
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Residues in contact with MET3648 (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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2004B GLN* 6.4 1.6 - - - -
2007B ILE* 4.6 22.4 - - + +
2008B ASN* 5.4 0.3 - - - +
3644B ARG 3.3 11.1 + - - +
3645B ALA* 3.3 14.0 + - - +
3646B CYS 3.2 0.8 - - - -
3647B ASN* 1.3 78.6 - - - +
3649B PHE* 1.3 60.5 + - - +
3650B LEU 3.4 0.3 + - - -
3651B GLU* 3.6 7.9 + - - +
3652B SER* 3.5 18.5 + - - -
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Residues in contact with PHE3649 (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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1962B PHE* 5.4 4.7 - + - -
1963B ALA* 3.6 33.4 - - + -
1966B TYR* 3.7 34.5 - + + -
1967B VAL* 4.9 14.8 - - + -
1970B LEU* 5.2 3.1 - - + -
2007B ILE* 4.9 8.7 - - + +
2010B LEU* 6.3 0.2 - - + -
2011B LEU* 3.9 30.3 - - + -
2032B LEU* 4.6 9.0 - - + -
3645B ALA 3.7 4.1 + - - +
3646B CYS 3.3 13.3 + - - +
3647B ASN 3.2 1.0 - - - -
3648B MET* 1.3 76.3 - - - +
3650B LEU* 1.3 61.4 + - + +
3652B SER* 3.9 5.2 - - - +
3653B TYR* 3.0 57.4 + + + +
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Residues in contact with LEU3650 (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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1959B LEU* 3.6 31.2 - - + -
1960B ALA* 5.3 9.2 - - + -
1963B ALA* 4.5 15.0 - - + -
2139B LEU* 4.4 29.2 - - + +
2142B ALA* 3.9 37.9 - - + +
2143B TYR* 4.6 5.6 - - - +
2144B THR* 4.9 8.7 - - - +
3646B CYS 4.1 7.2 + - - +
3647B ASN* 3.3 15.3 + - - +
3648B MET 3.2 0.8 - - - -
3649B PHE* 1.3 80.9 - - + +
3651B GLU* 1.3 60.8 + - - +
3653B TYR* 3.5 12.5 + - + +
3654B LYS* 3.6 11.6 + - - +
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Residues in contact with GLU3651 (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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3647B ASN 4.0 3.9 + - - +
3648B MET* 3.6 9.0 + - - +
3649B PHE 3.4 0.2 - - - -
3650B LEU* 1.3 79.6 - - - +
3652B SER* 1.3 63.3 + - - +
3654B LYS* 3.4 18.2 + - - +
3655B ALA* 4.2 4.2 + - - +
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Residues in contact with SER3652 (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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2007B ILE* 4.9 7.6 - - - -
2008B ASN* 3.3 32.1 - - - -
2011B LEU* 5.0 10.5 - - - -
3648B MET 3.5 12.5 + - - -
3649B PHE* 3.5 7.7 + - - -
3650B LEU 3.4 0.2 - - - -
3651B GLU* 1.3 79.1 - - - +
3653B TYR* 1.3 63.3 + - - +
3654B LYS 3.3 0.2 + - - -
3655B ALA* 3.6 4.8 + - - +
3656B ALA* 3.3 22.4 + - - +
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Residues in contact with TYR3653 (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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1959B LEU* 4.4 27.9 - - + +
1962B PHE* 5.9 2.9 - + - -
2032B LEU* 4.7 13.9 - - + -
2035B PHE* 5.5 5.4 - + - -
2036B HIS* 3.1 35.9 - + - +
2039B LEU* 5.1 7.7 - - + +
2135B LEU* 6.0 0.7 - - + -
2139B LEU* 5.6 7.6 - - + -
3649B PHE* 3.0 47.5 + + + +
3650B LEU* 3.9 8.1 - - + +
3651B GLU 3.3 0.4 - - - -
3652B SER* 1.3 73.8 - - - +
3654B LYS* 1.3 66.0 + - - +
3656B ALA* 3.4 11.7 + - + -
3657B TRP* 3.6 28.9 + + + -
3658B ILE* 3.4 31.4 - - + +
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Residues in contact with LYS3654 (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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2136B LEU* 6.1 4.0 - - + -
2139B LEU* 4.1 21.5 - - + +
3650B LEU 3.6 5.7 + - - +
3651B GLU* 3.4 13.6 + - - +
3652B SER 3.2 0.6 - - - -
3653B TYR* 1.3 78.5 - - - +
3655B ALA* 1.3 58.9 + - + +
3656B ALA 3.5 0.3 + - - -
3658B ILE* 3.2 15.9 - - + +
3659B LEU* 3.1 34.3 + - + +
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Residues in contact with ALA3655 (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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3651B GLU 4.2 3.7 + - - +
3652B SER* 3.6 6.5 + - - +
3654B LYS* 1.3 77.6 - - + +
3656B ALA* 1.3 62.2 + - - +
3659B LEU* 3.8 27.3 - - + +
3660B THR* 5.2 3.6 - - - +
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Residues in contact with ALA3656 (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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2011B LEU* 5.3 8.7 - - + +
2012B HIS* 6.0 7.0 - - - +
2013B PHE 6.4 0.2 - - - +
3652B SER 3.3 17.6 + - - +
3653B TYR* 3.8 10.1 - - + +
3654B LYS 3.2 1.2 - - - -
3655B ALA* 1.3 78.7 - - - +
3657B TRP* 1.3 87.9 + - + +
3660B THR* 3.3 16.8 - - - +
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Residues in contact with TRP3657 (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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2011B LEU 5.1 4.0 + - - -
2013B PHE* 3.2 60.0 - + + +
2014B LYS* 4.5 6.5 - - + -
2032B LEU* 4.4 20.1 - - + +
2033B LEU* 5.8 8.3 - - + -
2036B HIS* 3.3 48.1 + + + +
3653B TYR* 3.6 27.3 + + + +
3656B ALA* 1.3 97.8 - - + +
3658B ILE* 1.3 63.5 + - - +
3659B LEU 3.8 0.4 - - - -
3660B THR* 3.9 13.2 - - + -
3661B GLU* 3.3 25.4 - - + +
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Residues in contact with ILE3658 (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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2036B HIS* 5.0 4.3 - - + +
2039B LEU* 5.5 6.7 - - + -
2040B LEU* 5.9 2.5 - - + -
2132B LEU* 4.8 13.0 - - + +
2135B LEU* 4.1 28.9 - - + -
2136B LEU* 4.0 28.5 - - + +
2139B LEU* 5.1 4.7 - - + -
3653B TYR* 3.4 45.3 - - + +
3654B LYS* 3.2 13.6 + - - +
3657B TRP* 1.3 84.5 - - + +
3659B LEU* 1.3 62.8 + - - +
3660B THR 3.2 5.1 + - - -
3661B GLU* 3.6 15.5 + - - +
3662B ASP* 4.2 3.3 + - - +
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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