Contacts of the helix formed by residues 4907 - 4922 (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 TYR4907 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4856B PHE* 4.7 37.2 - + + -
4857B PHE* 4.8 11.0 - + + -
4859B LYS* 5.9 5.8 - - - -
4860B PHE* 4.7 8.0 - + + -
4905B ASP 3.3 2.2 + - - -
4906B GLU* 1.3 78.9 - - + +
4908B GLU* 1.3 64.0 + - - +
4909B LEU 3.6 0.9 - - - -
4910B TYR* 3.9 29.8 - + + -
4911B ARG* 3.2 21.7 + - - +
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Residues in contact with GLU4908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4860B PHE* 6.3 0.2 - - - -
4902B PRO* 5.3 11.9 - - - +
4904B GLY 3.4 22.4 - - - +
4905B ASP* 3.5 12.8 + - - +
4906B GLU 3.2 0.8 - - - -
4907B TYR* 1.3 79.0 - - - +
4909B LEU* 1.3 63.9 + - - +
4911B ARG* 3.9 2.8 - - - +
4912B VAL* 3.3 26.9 + - - +
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Residues in contact with LEU4909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4908B GLU* 1.3 78.1 - - - +
4910B TYR* 1.3 63.3 + - - +
4912B VAL* 3.4 9.5 + - - +
4913B VAL* 3.3 25.7 + - - +
4882D LEU* 5.4 9.9 - - + -
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Residues in contact with TYR4910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4852B VAL* 5.9 2.1 - - - +
4856B PHE* 4.9 23.6 - + - -
4857B PHE* 3.7 30.1 - + - -
4907B TYR* 3.9 31.5 - + + +
4908B GLU 3.2 0.8 - - - -
4909B LEU* 1.3 79.7 - - - +
4911B ARG* 1.3 60.1 + - - +
4913B VAL* 3.3 23.3 - - + +
4914B PHE* 3.3 15.8 + + + +
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Residues in contact with ARG4911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4857B PHE* 4.1 16.4 - - + -
4860B PHE* 4.1 24.0 - - + -
4902B PRO* 5.3 10.8 - - + -
4907B TYR 3.2 20.3 + - - +
4908B GLU* 3.9 3.6 - - - +
4910B TYR* 1.3 74.9 - - - +
4912B VAL* 1.3 64.0 + - - +
4913B VAL 3.5 0.2 - - - -
4914B PHE* 3.6 5.2 + - + +
4915B ASP* 3.3 21.7 + - - +
4886D TYR* 4.6 2.3 + - - -
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Residues in contact with VAL4912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4902B PRO* 5.2 13.2 - - + -
4908B GLU 3.3 17.5 + - - +
4909B LEU* 3.7 9.2 - - - +
4910B TYR 3.3 0.4 - - - -
4911B ARG* 1.3 77.1 - - + +
4913B VAL* 1.3 67.3 + - + +
4914B PHE 3.3 0.2 + - - -
4915B ASP 3.4 2.3 + - - -
4916B ILE* 3.2 29.6 + - + +
4882D LEU* 3.8 39.9 - - + -
4886D TYR* 3.5 38.0 - - + -
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Residues in contact with VAL4913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4909B LEU 3.3 12.2 + - - +
4910B TYR* 3.3 28.0 - - + +
4912B VAL* 1.3 81.3 - - - +
4914B PHE* 1.3 62.6 + - - +
4916B ILE* 3.3 9.9 + - + +
4917B THR* 3.2 26.9 + - + +
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Residues in contact with PHE4914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4849B TYR* 3.5 46.0 - + + -
4852B VAL* 4.2 13.5 - - + -
4853B ALA* 5.3 0.4 - - + -
4857B PHE* 3.5 37.2 - + + -
4861B TYR* 4.4 16.4 - - - -
4884B HIS* 6.2 0.2 - + - -
4895B ILE* 4.5 15.7 - - + -
4899B ILE* 6.5 0.2 - - + -
4910B TYR* 3.3 19.0 + + + +
4911B ARG* 3.7 9.2 - - + +
4912B VAL 3.2 0.6 - - - -
4913B VAL* 1.3 84.0 - - + +
4915B ASP* 1.3 61.3 + - + +
4917B THR* 3.3 10.4 - - + +
4918B PHE* 3.1 35.6 + + + +
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Residues in contact with ASP4915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4895B ILE* 4.1 22.0 + - + +
4896B GLY 5.1 3.1 - - - +
4899B ILE* 5.6 1.3 - - + -
4911B ARG 3.3 8.5 + - - +
4914B PHE* 1.3 82.0 - - + +
4916B ILE* 1.3 61.7 + - - +
4918B PHE* 3.7 9.0 - - - +
4919B PHE* 3.0 28.6 + - - +
4886D TYR* 3.6 33.9 - - + +
4890D ARG* 5.5 1.8 - - - +
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Residues in contact with ILE4916 (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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4912B VAL* 3.2 20.9 + - + +
4913B VAL* 3.6 13.7 - - + +
4914B PHE 3.2 0.4 - - - -
4915B ASP* 1.3 78.3 - - - +
4917B THR* 1.3 63.8 + - - +
4919B PHE* 3.3 6.4 + - + +
4920B PHE* 3.1 51.5 + - + -
4885D MET* 4.1 21.5 - - + +
4886D TYR* 3.7 42.2 - - + +
4889D VAL* 5.5 1.3 - - + -
4890D ARG* 5.0 7.9 - - + +
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Residues in contact with THR4917 (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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4849B TYR* 3.6 18.4 + - + +
4913B VAL* 3.2 21.2 + - + +
4914B PHE* 3.3 15.5 - - + +
4916B ILE* 1.3 80.2 - - - +
4918B PHE* 1.3 63.0 + - - +
4920B PHE* 4.3 8.7 - - - -
4921B PHE* 3.1 48.2 + - - +
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Residues in contact with PHE4918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4846B VAL* 4.5 13.9 - - + -
4849B TYR* 3.8 39.7 - + + -
4884B HIS* 5.3 13.2 - - + -
4888B GLY* 5.3 7.6 - - - -
4894B GLY* 4.8 4.5 - - - -
4895B ILE* 3.7 52.0 - - + -
4914B PHE* 3.1 31.6 + + + +
4915B ASP* 3.7 6.7 - - - +
4916B ILE 3.2 0.2 - - - -
4917B THR* 1.3 78.8 - - - +
4919B PHE* 1.3 61.2 + - - +
4920B PHE 3.6 0.2 + - - -
4921B PHE* 5.2 0.2 - - - -
4922B VAL* 3.2 57.3 + - + +
4923B ILE* 3.6 0.8 - - + +
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Residues in contact with PHE4919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4892B GLY 4.2 7.6 - - - -
4894B GLY* 4.5 11.0 - - - -
4915B ASP 3.0 17.2 + - - +
4916B ILE* 3.3 5.4 + - + +
4918B PHE* 1.3 76.8 - - - +
4920B PHE* 1.3 82.4 + + - +
4923B ILE* 3.4 42.8 - - + +
4924B VAL* 3.4 20.9 - - + +
4889D VAL* 3.2 37.9 - - + -
4890D ARG* 3.5 35.7 - - + -
4892D GLY* 5.7 2.2 - - - -
4927D LEU* 4.7 14.8 - - + -
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Residues in contact with PHE4920 (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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4916B ILE* 3.1 41.0 + - + +
4917B THR* 3.4 8.9 + - - +
4918B PHE 3.3 0.2 - - - -
4919B PHE* 1.3 104.1 - + - +
4921B PHE* 1.3 66.0 + - + +
4924B VAL* 3.2 29.3 - - + +
4925B ILE* 3.4 11.6 - - - +
4839D VAL* 6.2 6.1 - - + -
4842D LEU* 5.3 9.4 - - + -
4885D MET* 4.2 16.4 - - + -
4889D VAL* 3.7 23.1 - - + -
4927D LEU* 6.0 1.8 - - + -
4930D ILE* 6.1 4.4 - - + +
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Residues in contact with PHE4921 (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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4845B VAL* 6.6 0.2 - - + -
4849B TYR* 4.3 13.7 - + + +
4917B THR* 3.1 42.7 + - - +
4918B PHE* 4.6 0.9 - - - +
4919B PHE 3.4 0.2 - - - -
4920B PHE* 1.3 84.8 - - + +
4922B VAL* 1.3 69.8 + - + +
4923B ILE 3.3 0.4 - - - -
4925B ILE* 3.0 24.2 + - + +
4926B LEU* 2.9 24.8 + - - +
4828D VAL* 4.8 23.3 - - + -
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Residues in contact with VAL4922 (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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4842B LEU* 5.4 3.3 - - + +
4845B VAL* 4.0 30.3 - - + -
4846B VAL* 4.4 9.6 - - + -
4849B TYR* 4.9 4.7 - - + -
4888B GLY 6.4 1.6 - - - -
4889B VAL* 6.3 4.7 - - + -
4918B PHE* 3.2 49.3 + - + +
4921B PHE* 1.3 81.9 - - + +
4923B ILE* 1.3 71.9 + - + +
4926B LEU* 3.3 25.1 - - + +
4927B LEU* 3.4 17.0 - - - +
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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