Contacts of the helix formed by residues 3641 - 3658 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3639H ASN 4.5 1.8 - - - +
3640H LEU* 1.3 84.4 - - + +
3642H THR* 1.3 65.6 + - - +
3643H HIS* 3.1 6.6 + - + +
3644H ARG* 4.0 13.1 - - + +
3645H ALA* 3.1 24.0 + - - +
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Residues in contact with THR3642 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967H VAL* 5.5 5.0 - - - +
1968H ASP* 5.7 5.9 - - - +
1971H GLN* 4.4 16.4 + - - -
3640H LEU 3.1 6.4 + - - -
3641H PRO* 1.3 69.0 - - - +
3643H HIS* 1.3 67.8 + - + +
3645H ALA* 3.8 9.2 - - - +
3646H CYS* 3.3 22.7 + - - +
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Residues in contact with HIS3643 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2144H THR* 3.8 20.2 - - - +
2145H ILE 4.5 4.9 - - - +
2146H SER* 4.0 35.0 - - - +
2195H HIS* 4.7 10.8 - - + -
3641H PRO* 3.1 4.8 - - + -
3642H THR* 1.3 86.5 - - + +
3644H ARG* 1.3 61.1 + - - +
3646H CYS* 3.7 9.1 + - - +
3647H ASN 3.8 5.0 + - - -
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Residues in contact with ARG3644 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2143H TYR* 5.1 10.1 - - - +
2144H THR 5.4 0.2 - - - -
2195H HIS* 5.1 7.8 - - + +
3641H PRO* 3.5 16.2 + - + +
3643H HIS* 1.3 77.7 - - - +
3645H ALA* 1.3 65.3 + - - +
3646H CYS 3.3 0.2 - - - -
3647H ASN* 3.5 8.6 + - - +
3648H MET* 3.3 19.8 + - - +
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Residues in contact with ALA3645 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967H VAL* 3.8 22.9 - - + +
1971H GLN* 5.3 4.9 - - - +
2007H ILE* 5.5 5.7 - - + +
3637H LEU* 5.0 13.5 - - + -
3640H LEU* 5.3 7.0 - - + -
3641H PRO 3.1 19.5 + - - +
3642H THR* 4.1 9.2 - - - +
3643H HIS 3.3 0.2 - - - -
3644H ARG* 1.3 75.2 - - - +
3646H CYS* 1.3 65.0 + - - +
3648H MET* 3.3 18.6 + - - +
3649H PHE* 3.7 4.2 + - - +
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Residues in contact with CYS3646 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1963H ALA* 4.9 5.4 - - - +
1964H GLU* 4.4 15.3 - - + +
1967H VAL* 3.8 25.7 - - + +
2144H THR* 4.3 19.9 + - + +
3642H THR* 3.3 16.2 + - - +
3643H HIS 3.7 4.5 + - - +
3644H ARG 3.3 0.2 - - - -
3645H ALA* 1.3 78.1 - - - +
3647H ASN* 1.3 62.6 + - - +
3649H PHE* 3.3 17.3 + - - +
3650H LEU* 4.1 6.9 + - - +
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Residues in contact with ASN3647 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2143H TYR* 3.8 35.9 - - + +
2144H THR* 4.2 23.9 - - - +
3643H HIS 3.8 4.2 + - - +
3644H ARG* 3.5 9.3 + - - +
3645H ALA 3.3 0.6 - - - -
3646H CYS* 1.3 78.8 - - - +
3648H MET* 1.3 62.3 + - - +
3650H LEU* 3.3 23.2 + - + +
3651H GLU* 4.0 4.0 + - - +
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Residues in contact with MET3648 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004H GLN* 6.4 1.8 - - - -
2007H ILE* 4.6 22.7 - - + +
3644H ARG 3.3 10.6 + - - +
3645H ALA* 3.3 14.2 + - - +
3646H CYS 3.2 0.8 - - - -
3647H ASN* 1.3 79.3 - - - +
3649H PHE* 1.3 60.8 + - - +
3650H LEU 3.2 0.7 + - - -
3651H GLU* 3.6 8.1 + - - +
3652H SER* 3.5 18.5 + - - -
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Residues in contact with PHE3649 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962H PHE* 5.4 4.7 - + - -
1963H ALA* 3.6 32.8 - - + -
1966H TYR* 3.7 34.5 - + + -
1967H VAL* 4.9 14.4 - - + -
1970H LEU* 5.2 2.9 - - + -
2007H ILE* 4.9 9.3 - - + +
2010H LEU* 6.3 0.2 - - + -
2011H LEU* 3.8 30.3 - - + -
2032H LEU* 4.6 8.5 - - + -
3645H ALA 3.7 5.5 + - - +
3646H CYS 3.3 12.9 + - - +
3647H ASN 3.2 1.0 - - - -
3648H MET* 1.3 76.3 - - - +
3650H LEU* 1.3 61.8 + - + +
3651H GLU 3.4 0.2 - - - -
3652H SER* 3.5 5.1 + - - +
3653H TYR* 3.0 58.0 + + + +
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Residues in contact with LEU3650 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1959H LEU* 3.6 30.3 - - + -
1960H ALA* 5.3 9.2 - - + -
1963H ALA* 4.5 15.9 - - + -
2139H LEU* 4.4 29.5 - - + +
2142H ALA* 3.9 38.1 - - + +
2143H TYR* 4.6 5.2 - - - +
2144H THR* 4.9 9.2 - - - +
3646H CYS 4.6 6.7 - - - +
3647H ASN* 3.3 14.9 + - + +
3648H MET 3.2 0.6 - - - -
3649H PHE* 1.3 80.6 - - + +
3651H GLU* 1.3 61.0 + - - +
3653H TYR* 3.5 12.4 + - + +
3654H LYS* 3.6 11.8 + - - +
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Residues in contact with GLU3651 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3647H ASN 4.0 3.8 + - - +
3648H MET* 3.6 10.3 + - - +
3649H PHE 3.4 0.4 - - - -
3650H LEU* 1.3 78.5 - - - +
3652H SER* 1.3 63.2 + - - +
3654H LYS* 3.4 18.7 + - - +
3655H ALA* 4.2 3.8 + - - +
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Residues in contact with SER3652 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007H ILE* 4.9 7.6 - - - -
2008H ASN* 3.3 33.2 - - - -
2011H LEU* 5.0 10.1 - - - -
3648H MET 3.5 13.2 + - - -
3649H PHE* 3.5 8.4 + - - -
3650H LEU 3.4 0.4 - - - -
3651H GLU* 1.3 77.7 - - - +
3653H TYR* 1.3 63.7 + - - +
3654H LYS 3.3 0.2 + - - -
3655H ALA* 3.6 5.0 + - - +
3656H ALA* 3.3 22.2 + - - +
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Residues in contact with TYR3653 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1959H LEU* 4.4 26.0 - - + +
1962H PHE* 5.9 2.7 - + - -
2032H LEU* 4.7 13.9 - - + -
2035H PHE* 5.5 5.2 - + - -
2036H HIS* 3.1 36.2 - + + +
2039H LEU* 5.1 8.6 - - + +
2135H LEU* 6.0 0.4 - - + -
2139H LEU* 5.6 7.4 - - + -
3649H PHE* 3.0 47.7 + + + +
3650H LEU* 3.9 9.0 - - + +
3651H GLU 3.3 0.6 - - - -
3652H SER* 1.3 74.0 - - - +
3654H LYS* 1.3 65.0 + - - +
3655H ALA 3.5 0.2 - - - -
3656H ALA* 3.4 10.7 + - + -
3657H TRP* 3.6 28.6 + + - -
3658H ILE* 3.4 32.7 - - + +
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Residues in contact with LYS3654 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2136H LEU* 5.8 3.8 - - + +
2139H LEU* 4.1 20.9 - - + -
3650H LEU 3.6 6.3 + - - +
3651H GLU* 3.4 13.8 + - - +
3652H SER 3.2 0.8 - - - -
3653H TYR* 1.3 78.6 - - - +
3655H ALA* 1.3 58.4 + - + +
3656H ALA 3.2 0.4 + - - -
3658H ILE* 3.2 14.7 - - + +
3659H LEU* 3.1 37.1 + - + +
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Residues in contact with ALA3655 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3651H GLU 4.2 3.9 + - - +
3652H SER* 3.6 6.4 + - - +
3654H LYS* 1.3 76.3 - - + +
3656H ALA* 1.3 61.4 + - - +
3659H LEU* 3.8 26.9 - - + +
3660H THR* 5.2 3.9 - - - +
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Residues in contact with ALA3656 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011H LEU* 5.3 9.0 - - + +
2012H HIS* 6.0 7.0 - - - +
3652H SER 3.3 18.2 + - - +
3653H TYR* 3.8 10.1 - - + +
3654H LYS 3.2 1.4 - - - -
3655H ALA* 1.3 79.5 - - - +
3657H TRP* 1.3 87.5 + - + +
3658H ILE 3.8 0.2 - - - -
3660H THR* 3.3 16.4 - - - +
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Residues in contact with TRP3657 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011H LEU 5.1 4.6 + - - -
2013H PHE* 3.2 60.3 - + + +
2014H LYS* 4.5 6.7 - - + -
2032H LEU* 4.4 18.8 - - + +
2033H LEU* 5.8 8.1 - - + -
2036H HIS* 3.3 48.5 + + + +
3653H TYR* 3.6 27.7 + + + +
3656H ALA* 1.3 97.5 - - + +
3658H ILE* 1.3 64.7 + - - +
3659H LEU 3.8 0.2 - - - -
3660H THR* 3.9 13.7 - - + -
3661H GLU* 3.3 24.8 - - + +
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Residues in contact with ILE3658 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2036H HIS* 5.0 4.5 - - + +
2039H LEU* 5.5 6.1 - - + -
2040H LEU* 5.9 2.5 - - + -
2132H LEU* 4.8 12.3 - - + +
2135H LEU* 4.1 31.0 - - + -
2136H LEU* 4.0 28.3 - - + +
2139H LEU* 5.1 4.3 - - + -
3653H TYR* 3.4 44.2 - - + +
3654H LYS* 3.2 14.9 + - + +
3657H TRP* 1.3 84.3 - - + +
3659H LEU* 1.3 61.2 - - - +
3660H THR 3.2 5.9 + - - -
3661H GLU* 3.6 15.3 + - - +
3662H ASP* 4.2 3.5 + - - +
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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