Contacts of the helix formed by residues 4046 - 4067 (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 SER4046 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3985H VAL* 4.3 16.8 - - - -
3988H LEU* 5.5 6.3 - - - -
4042H MET 2.5 24.0 + - - -
4043H LEU* 3.3 12.6 - - - +
4044H VAL 3.3 0.2 - - - -
4045H GLU* 1.3 76.1 - - - +
4047H SER* 1.3 55.2 + - - +
4048H SER 3.3 2.9 - - - -
4049H ASN* 3.0 17.1 + - - +
4050H VAL* 2.7 49.2 + - - +
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Residues in contact with SER4047 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4043H LEU 2.6 22.9 + - - -
4044H VAL* 2.7 21.1 + - - +
4045H GLU 3.3 2.4 - - - -
4046H SER* 1.3 77.9 - - - +
4048H SER* 1.3 60.1 + - - +
4050H VAL* 3.4 21.1 - - - +
4051H GLU* 3.5 13.0 + - - +
4154H ARG* 6.1 0.3 - - - +
4161H LEU* 6.0 0.3 - - - +
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Residues in contact with SER4048 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4045H GLU 4.6 2.9 + - - -
4046H SER 3.3 0.6 - - - -
4047H SER* 1.3 80.0 - - - +
4049H ASN* 1.3 64.5 + - - +
4051H GLU* 4.1 7.0 + - - +
4052H MET* 3.4 23.2 + - - +
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Residues in contact with ASN4049 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3985H VAL* 4.8 8.8 - - - +
3988H LEU* 4.7 21.1 - - + +
3989H HIS* 3.2 37.6 + - - +
3992H ALA* 4.5 6.1 - - + +
4045H GLU 3.4 9.9 + - - -
4046H SER* 3.0 29.9 + - - +
4048H SER* 1.3 84.1 - - - +
4050H VAL* 1.3 65.6 + - + +
4051H GLU 3.2 1.6 - - - -
4052H MET* 3.3 19.4 + - - +
4053H ILE* 3.7 8.5 + - - +
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Residues in contact with VAL4050 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3988H LEU* 4.9 13.5 - - + -
4043H LEU* 5.0 13.9 - - + +
4046H SER* 2.7 42.0 + - - +
4047H SER* 3.4 16.2 - - - +
4049H ASN* 1.3 73.7 - - - +
4051H GLU* 1.3 61.0 + - + +
4052H MET 3.2 0.2 - - - -
4053H ILE* 3.4 10.5 - - + +
4054H LEU* 3.0 32.3 + - - +
4158H PHE* 5.5 11.7 - - + -
4161H LEU* 6.0 5.4 - - + -
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Residues in contact with GLU4051 (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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4047H SER 3.5 14.1 + - - +
4048H SER* 4.2 7.2 - - - +
4049H ASN 3.2 0.4 - - - -
4050H VAL* 1.3 82.6 - - + +
4052H MET* 1.3 67.2 + - + +
4053H ILE 3.4 0.2 - - - -
4054H LEU* 4.1 5.2 - - - -
4055H LYS* 3.5 24.3 + - - +
4161H LEU* 4.9 17.0 - - + -
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Residues in contact with MET4052 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3992H ALA* 3.8 25.2 - - + +
3993H HIS* 5.7 9.9 - - + +
3996H MET* 4.6 32.0 - - + +
4048H SER 3.4 20.2 - - - +
4049H ASN* 3.3 9.8 + - - +
4050H VAL 3.2 1.0 - - - -
4051H GLU* 1.3 84.2 - - - +
4053H ILE* 1.3 56.8 + - - +
4055H LYS* 5.0 1.0 - - - +
4056H PHE* 3.2 20.1 + - - +
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Residues in contact with ILE4053 (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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3988H LEU* 5.6 12.3 - - + -
3991H PHE 5.7 3.4 - - - +
3992H ALA* 5.2 10.1 - - + -
3995H MET* 5.6 6.3 - - + -
4049H ASN 3.8 10.3 - - - +
4050H VAL* 3.4 19.3 - - + +
4052H MET* 1.3 77.3 - - - +
4054H LEU* 1.3 70.0 + - + +
4055H LYS 3.4 0.2 - - - -
4056H PHE* 3.4 26.5 - - + +
4057H PHE* 3.1 44.7 + - + +
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Residues in contact with LEU4054 (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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4050H VAL 3.0 20.1 + - - +
4051H GLU* 4.5 4.9 - - - +
4053H ILE* 1.3 80.5 - - + +
4055H LYS* 1.3 56.8 + - - +
4057H PHE* 3.3 4.3 + - - +
4058H ASP* 2.8 38.2 + - - +
4161H LEU* 4.6 22.4 - - + +
4162H ALA* 5.1 8.5 - - + -
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Residues in contact with LYS4055 (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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4051H GLU 3.5 18.4 + - - +
4052H MET* 5.0 1.6 - - - +
4054H LEU* 1.3 77.3 - - - +
4056H PHE* 1.3 62.8 + - - +
4058H ASP* 4.3 7.6 - - - -
4059H MET* 3.2 26.5 + - - +
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Residues in contact with PHE4056 (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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3995H MET* 3.7 42.0 - - + -
3996H MET* 3.9 31.6 - - + -
3999H ALA* 4.6 6.1 - - + -
4052H MET 3.2 19.6 + - - +
4053H ILE* 3.2 20.7 + - + +
4054H LEU 3.2 0.6 - - - -
4055H LYS* 1.3 80.6 - - - +
4057H PHE* 1.3 82.6 + + - +
4059H MET* 4.5 1.4 - - - +
4060H PHE* 3.2 59.1 + + - -
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Residues in contact with PHE4057 (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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4012H LEU* 4.3 15.7 - - + -
4053H ILE* 3.1 31.2 + - + +
4054H LEU* 4.0 4.3 - - - +
4056H PHE* 1.3 105.8 - + - +
4058H ASP* 1.3 57.4 + - - +
4059H MET 3.2 1.8 - - - -
4060H PHE* 3.3 8.2 + + + +
4061H LEU* 2.7 38.5 + - - +
4131H ALA* 4.9 15.0 - - + -
4134H ILE* 3.6 47.1 - - + -
4135H GLY* 4.8 10.1 - - - -
4138H VAL* 5.0 9.2 - - + -
4165H ILE* 6.0 3.4 - - + -
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Residues in contact with ASP4058 (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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4054H LEU* 2.8 22.1 + - - +
4055H LYS* 4.3 6.4 - - - -
4057H PHE* 1.3 79.1 - - - +
4059H MET* 1.3 60.7 + - - +
4061H LEU* 4.0 7.0 - - - +
4062H LYS* 3.2 23.4 + - - +
4161H LEU 3.0 26.7 - - - +
4162H ALA* 4.1 3.8 - - - +
4164H SER* 3.9 24.9 - - - -
4165H ILE* 3.9 24.4 + - - +
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Residues in contact with MET4059 (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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4055H LYS 3.2 21.0 + - - +
4056H PHE* 4.5 2.7 - - - +
4058H ASP* 1.3 78.9 - - - +
4060H PHE* 1.3 68.8 + - + +
4062H LYS* 3.4 6.7 + - - +
4063H LEU* 3.3 26.3 + - - +
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Residues in contact with PHE4060 (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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3999H ALA* 5.1 10.5 - - + -
4056H PHE* 3.2 57.9 + + - +
4057H PHE* 3.3 10.5 + + + +
4059H MET* 1.3 81.0 - - + +
4061H LEU* 1.3 64.8 + - - +
4063H LEU* 3.3 37.7 + - + +
4064H LYS* 3.9 4.3 + - - +
4127H PHE* 3.5 42.8 - + + -
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Residues in contact with LEU4061 (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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4057H PHE 2.7 22.3 + - - +
4058H ASP* 4.0 6.1 - - - +
4060H PHE* 1.3 74.1 - - - +
4062H LYS* 1.3 60.8 + - - +
4064H LYS* 3.5 18.1 + - + +
4065H ASP* 4.4 1.6 + - - +
4164H SER* 3.3 36.8 - - - +
4165H ILE* 4.0 8.7 - - + +
4168H TYR* 3.6 50.3 - - + -
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Residues in contact with LYS4062 (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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4058H ASP 3.2 18.6 + - - +
4059H MET* 3.8 5.8 - - - +
4060H PHE 3.2 0.2 - - - -
4061H LEU* 1.3 72.5 - - - +
4063H LEU* 1.3 59.7 + - + +
4064H LYS 3.1 2.9 - - - -
4065H ASP* 2.8 25.1 + - - +
4066H ILE* 3.1 25.9 + - + +
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Residues in contact with LEU4063 (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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4059H MET 3.3 13.0 - - - +
4060H PHE* 3.3 38.9 + - + +
4062H LYS* 1.3 77.4 - - + +
4064H LYS* 1.3 60.7 + - - +
4065H ASP 3.2 0.9 + - - -
4066H ILE* 4.0 16.3 - - + +
4067H VAL* 3.5 24.4 + - - +
4124H ALA* 4.8 18.9 - - + +
4125H ASN* 5.0 2.7 + - - -
4127H PHE* 5.4 3.6 - - + -
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Residues in contact with LYS4064 (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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4060H PHE 3.9 4.4 + - - +
4061H LEU* 3.5 17.8 + - + +
4062H LYS 3.1 0.4 - - - -
4063H LEU* 1.3 78.3 - - - +
4065H ASP* 1.3 58.1 + - + +
4067H VAL* 3.6 15.6 - - + +
4068H GLY* 4.3 3.3 + - - -
4125H ASN* 3.4 34.9 - - - +
4128H GLN* 6.1 4.5 - - + +
4168H TYR* 4.9 19.1 + - + +
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Residues in contact with ASP4065 (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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4061H LEU 4.4 1.3 + - - +
4062H LYS* 2.8 11.4 + - - +
4064H LYS* 1.3 78.6 - - + +
4066H ILE* 1.3 64.0 + - + +
4067H VAL 3.3 1.8 - - - -
4068H GLY* 3.3 2.7 + - - +
4069H SER* 3.0 31.3 + - - -
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Residues in contact with ILE4066 (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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4062H LYS* 3.1 30.9 + - + +
4063H LEU* 3.6 17.4 + - + +
4065H ASP* 1.3 81.4 - - + +
4067H VAL* 1.3 61.8 + - - +
4069H SER* 2.8 22.2 + - - +
4071H ALA* 5.3 5.6 - - + -
4072H PHE* 3.3 25.2 - - + +
4090H LYS* 5.9 4.0 - - + -
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Residues in contact with VAL4067 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4063H LEU 3.5 17.0 + - - +
4064H LYS* 3.6 15.3 - - + +
4066H ILE* 1.3 78.5 - - - +
4068H GLY* 1.3 62.6 + - - +
4069H SER 4.4 3.0 - - - +
4072H PHE* 4.5 10.0 - - + +
4073H GLN* 5.5 1.9 + - - +
4124H ALA* 4.2 22.2 - - + -
4125H ASN* 4.5 13.5 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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