Contacts of the helix formed by residues 4152 - 4162 (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 ASP4152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4040B VAL* 5.4 9.0 - - + -
4149B VAL* 4.1 18.7 - - + +
4151B HIS* 1.3 76.3 - - - +
4153B PRO* 1.3 70.9 - - + +
4154B ARG* 3.2 2.2 - - + +
4155B LEU* 3.2 30.9 + - + +
4156B ARG* 3.3 13.2 + - - +
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Residues in contact with PRO4153 (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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4151B HIS 4.4 3.1 - - - +
4152B ASP* 1.3 84.2 - - + +
4154B ARG* 1.3 61.2 + - - +
4156B ARG* 3.5 6.7 + - + +
4157B ASN* 3.2 21.8 + - - +
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Residues in contact with ARG4154 (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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4040B VAL* 5.1 6.7 - - + +
4043B LEU* 4.9 11.9 - - + +
4044B VAL* 4.4 23.6 - - + +
4047B SER* 6.1 0.2 - - - +
4152B ASP* 3.2 3.2 - - + +
4153B PRO* 1.3 78.7 - - - +
4155B LEU* 1.3 65.3 + - - +
4157B ASN* 3.4 7.1 + - - +
4158B PHE* 3.1 23.9 + - - +
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Residues in contact with LEU4155 (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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4040B VAL* 5.5 5.6 - - + +
4043B LEU* 5.4 4.9 - - - -
4145B LEU* 5.4 8.1 - - + +
4146B SER* 4.4 28.6 - - - +
4149B VAL* 4.6 4.5 - - + -
4152B ASP* 3.2 26.4 + - + +
4154B ARG* 1.3 79.1 - - - +
4156B ARG* 1.3 56.1 + - - +
4158B PHE* 3.5 4.3 + - - +
4159B LEU* 3.0 29.6 + - - +
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Residues in contact with ARG4156 (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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4152B ASP 3.3 10.5 + - - +
4153B PRO* 4.0 8.1 - - + +
4155B LEU* 1.3 78.9 - - - +
4157B ASN* 1.3 57.6 + - - +
4159B LEU* 4.0 5.5 - - - +
4160B GLU* 3.0 29.5 + - - +
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Residues in contact with ASN4157 (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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4153B PRO 3.2 17.1 + - - +
4154B ARG* 3.7 8.1 - - - +
4155B LEU 3.2 0.4 - - - -
4156B ARG* 1.3 75.7 - - - +
4158B PHE* 1.3 65.2 + - - +
4160B GLU* 3.3 5.6 + - - +
4161B LEU* 3.1 41.9 + - - +
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Residues in contact with PHE4158 (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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4043B LEU* 3.9 25.4 - - + -
4050B VAL* 5.5 11.0 - - + -
4142B LEU* 6.5 0.4 - - - -
4154B ARG 3.1 16.0 + - - +
4155B LEU* 4.1 3.4 - - - +
4157B ASN* 1.3 76.5 - - - +
4159B LEU* 1.3 61.9 + - - +
4161B LEU* 3.6 8.8 + - - +
4162B ALA* 3.2 24.8 + - - +
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Residues in contact with LEU4159 (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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4142B LEU* 5.5 12.8 - - + +
4146B SER* 5.5 9.2 - - - +
4155B LEU 3.0 18.0 + - - +
4156B ARG* 4.0 5.8 - - - +
4158B PHE* 1.3 74.5 - - - +
4160B GLU* 1.3 64.1 + - - +
4162B ALA* 3.4 6.2 + - - +
4163B GLU* 3.2 21.0 + - - +
4166B LEU* 4.0 12.9 - - + +
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Residues in contact with GLU4160 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4156B ARG 3.0 19.4 + - - +
4157B ASN* 3.3 6.0 + - - +
4159B LEU* 1.3 77.7 - - - +
4161B LEU* 1.3 65.7 + - + +
4163B GLU* 3.3 20.9 + - - +
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Residues in contact with LEU4161 (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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4047B SER 6.0 0.4 - - - +
4050B VAL* 6.0 4.7 - - + -
4051B GLU* 4.9 19.7 - - + -
4054B LEU* 4.6 13.5 - - + +
4058B ASP* 3.0 19.2 - - - +
4157B ASN* 3.1 32.2 + - - +
4158B PHE* 4.1 7.6 - - - +
4160B GLU* 1.3 79.5 - - + +
4162B ALA* 1.3 57.3 + - - +
4163B GLU 3.4 1.3 + - - -
4164B SER 5.0 0.2 + - - -
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Residues in contact with ALA4162 (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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4054B LEU* 5.1 9.9 - - + -
4058B ASP* 4.1 6.1 - - - +
4138B VAL* 5.7 8.5 - - + -
4142B LEU* 5.7 8.5 - - + -
4158B PHE 3.2 17.8 + - - +
4159B LEU* 3.4 7.6 - - - +
4160B GLU 3.2 0.8 - - - -
4161B LEU* 1.3 76.8 - - - +
4163B GLU* 1.3 62.7 + - - +
4164B SER 3.2 2.7 - - - -
4165B ILE* 3.3 20.3 + - + +
4166B LEU* 3.4 15.9 + - + +
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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
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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