Contacts of the helix formed by residues 4726 - 4735 (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 HIS4726 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4679H LEU 4.9 4.3 - - - -
4680H GLU 4.3 10.4 + - - -
4681H PHE* 4.1 24.4 + - - -
4682H ASP* 4.6 3.2 + - - -
4686H ILE* 4.1 33.3 - - + +
4687H THR* 4.3 16.5 - - + +
4688H GLU* 6.4 0.2 - - + -
4722H VAL* 3.1 14.3 + - + +
4725H LYS* 1.3 91.2 + - + +
4727H GLY* 1.3 59.7 + - - +
4728H ASP 3.5 2.2 + - - -
4729H ILE* 3.7 25.0 + - + +
4730H TYR* 4.5 3.1 + - - +
4735H ILE* 3.8 8.3 - - - +
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Residues in contact with GLY4727 (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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4722H VAL 3.5 4.6 + - - -
4723H LEU 3.3 21.5 + - - -
4724H ASP 4.3 0.2 - - - -
4725H LYS 3.4 2.4 - - - -
4726H HIS* 1.3 76.3 - - - +
4728H ASP* 1.3 60.2 + - - +
4729H ILE 3.2 2.0 - - - -
4730H TYR 4.4 0.2 - - - -
4731H GLY 3.1 35.6 + - - +
4732H ARG* 3.7 2.3 + - - -
4735H ILE* 3.7 20.2 - - - -
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Residues in contact with ASP4728 (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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4723H LEU 4.6 0.6 + - - -
4724H ASP 5.0 5.2 + - - +
4725H LYS 4.6 4.4 + - - +
4726H HIS* 3.5 0.8 - - - +
4727H GLY* 1.3 74.5 - - - +
4729H ILE* 1.3 70.7 + - + +
4731H GLY* 4.0 5.5 + - - -
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Residues in contact with ILE4729 (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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4071B ALA* 5.8 3.8 - - - +
4687H THR* 3.7 27.8 - - + +
4725H LYS 4.1 7.0 - - - +
4726H HIS* 3.7 34.8 - - + +
4727H GLY 3.2 0.6 - - - -
4728H ASP* 1.3 84.6 - - + +
4730H TYR* 1.3 75.9 + - + +
4731H GLY 3.3 0.8 + - - -
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Residues in contact with TYR4730 (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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4070B GLU* 4.7 13.7 - - + -
4686H ILE* 4.7 5.4 - - + -
4687H THR* 3.6 46.1 + - + -
4726H HIS 4.5 3.4 + - - +
4727H GLY 3.9 2.6 + - - +
4729H ILE* 1.3 93.9 - - + +
4731H GLY* 1.3 64.6 + - - +
4734H ARG* 3.3 70.6 + - + +
4735H ILE* 5.0 6.1 - - + +
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Residues in contact with GLY4731 (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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4727H GLY 3.1 19.6 + - - +
4728H ASP* 4.0 5.4 + - - -
4729H ILE 3.3 4.4 + - - -
4730H TYR* 1.3 82.2 - - - +
4732H ARG* 1.3 60.7 + - - -
4733H GLU* 3.1 8.1 + - - -
4735H ILE* 3.3 16.5 + - - +
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Residues in contact with ARG4732 (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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4723H LEU* 6.0 3.0 - - + +
4727H GLY 3.7 3.9 + - - -
4731H GLY* 1.3 70.5 - - - -
4733H GLU* 1.3 56.6 + - - +
4735H ILE* 4.0 10.6 - - - +
4736H ALA* 3.5 20.6 + - - +
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Residues in contact with GLU4733 (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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4730H TYR 5.7 0.2 - - - +
4731H GLY* 3.1 1.8 - - - -
4732H ARG* 1.3 77.9 - - - +
4734H ARG* 1.3 68.3 + - + +
4735H ILE 3.4 0.2 - - - -
4736H ALA* 3.5 5.5 + - - +
4737H GLU* 3.4 19.9 + - - +
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Residues in contact with ARG4734 (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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4070B GLU* 4.1 19.2 - - - +
4730H TYR* 3.3 67.1 + - + +
4731H GLY 3.8 1.6 + - - -
4733H GLU* 1.3 79.3 - - + +
4735H ILE* 1.3 62.8 + - - +
4736H ALA 3.4 0.2 + - - -
4737H GLU* 3.4 19.0 + - - +
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Residues in contact with ILE4735 (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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4686H ILE* 4.1 16.6 - - + -
4722H VAL* 3.5 41.1 - - + +
4723H LEU* 3.7 28.9 - - + +
4726H HIS 3.8 8.7 - - - +
4727H GLY* 3.7 20.4 - - - -
4730H TYR* 5.0 5.7 - - + +
4731H GLY 3.3 20.0 + - - +
4732H ARG* 4.0 11.7 - - - +
4734H ARG* 1.3 76.3 - - - +
4736H ALA* 1.3 67.0 + - - +
4737H GLU 4.4 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