Contacts of the helix formed by residues 4876 - 4892 (chain D) 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 ASP4876 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4854D PHE* 4.8 0.4 - - - -
4873D LYS 2.9 19.0 + - - +
4874D CYS 4.7 2.5 - - - -
4875D ASP* 1.3 79.8 - - + +
4877D MET* 1.3 64.2 + - - +
4878D MET* 3.2 4.7 - - + +
4879D THR* 3.3 29.3 + - - +
4880D CYS* 3.5 5.9 + - - -
4578F TYR 3.8 5.4 - - - +
4579F LYS* 4.7 3.1 - - + -
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Residues in contact with MET4877 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4850D THR* 4.6 5.0 - - - +
4854D PHE* 4.5 23.8 - - + -
4876D ASP* 1.3 72.3 - - - +
4878D MET* 1.3 58.7 + - - +
4879D THR 3.4 0.2 - - - -
4880D CYS* 3.8 6.5 + - - +
4881D TYR* 3.8 15.9 + - - +
4575F LEU 3.6 16.4 - - - +
4576F LEU* 3.3 19.5 - - - +
4578F TYR* 2.9 24.4 + - + +
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Residues in contact with MET4878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4876D ASP* 3.2 4.8 - - + +
4877D MET* 1.3 77.4 - - - +
4879D THR* 1.3 63.2 + - - +
4880D CYS 3.3 0.9 - - - -
4881D TYR* 3.3 25.8 + - + +
4882D LEU* 3.3 23.5 + - + +
4573F PHE* 6.3 2.9 - - + -
4576F LEU* 2.9 33.9 + - - +
4577F PHE* 5.3 16.2 - - + -
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Residues in contact with THR4879 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4873D LYS* 3.7 31.2 - - + -
4876D ASP* 3.3 19.9 + - - +
4878D MET* 1.3 76.6 - - - +
4880D CYS* 1.3 60.5 + - - +
4882D LEU* 3.4 8.3 + - + +
4883D PHE* 2.9 29.3 + - + +
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Residues in contact with CYS4880 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4850D THR* 3.9 19.3 - - + +
4853D ALA* 6.0 1.6 - - - -
4854D PHE* 4.9 17.0 - - + -
4861D TYR* 5.9 5.8 - - - -
4873D LYS* 3.1 37.7 - - - -
4874D CYS* 3.7 11.9 - - - -
4876D ASP 3.5 7.5 + - - -
4877D MET* 4.0 6.1 - - - +
4878D MET 3.3 0.4 - - - -
4879D THR* 1.3 78.5 - - - +
4881D TYR* 1.3 56.3 + - - +
4883D PHE* 4.3 2.2 - - - -
4884D HIS* 2.9 48.7 + - + +
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Residues in contact with TYR4881 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4843D ALA* 3.2 40.8 + - - +
4846D VAL* 4.1 16.3 - - + +
4847D TYR* 4.1 28.0 - + + -
4850D THR* 3.9 22.1 - - + +
4877D MET 3.8 9.2 + - - +
4878D MET* 3.3 30.2 + - + +
4879D THR 3.3 0.6 - - - -
4880D CYS* 1.3 80.7 - - - +
4882D LEU* 1.3 60.6 + - + +
4884D HIS* 4.1 2.0 - - + +
4885D MET* 3.1 42.4 + - + +
4576F LEU* 6.4 0.4 - - + -
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Residues in contact with LEU4882 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4909B LEU* 5.4 11.0 - - + -
4912B VAL* 3.8 39.5 - - + -
4878D MET* 3.3 13.9 + - + +
4879D THR* 3.4 10.5 + - + +
4881D TYR* 1.3 82.5 - - + +
4883D PHE* 1.3 63.1 + - - +
4885D MET* 4.7 5.4 - - + +
4886D TYR* 3.1 29.7 + - + +
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Residues in contact with PHE4883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4861D TYR* 4.2 20.4 - + + -
4863D LYS* 4.6 23.3 - - + -
4871D ASP 5.3 5.4 - - - -
4873D LYS* 4.3 17.7 - - + -
4879D THR* 2.9 20.2 + - + +
4880D CYS 3.8 4.3 - - - +
4882D LEU* 1.3 77.9 - - - +
4884D HIS* 1.3 76.0 + + + +
4886D TYR* 5.0 0.2 - - - -
4887D VAL* 3.2 42.9 + - + +
4895D ILE* 5.4 2.2 - - + -
4898D GLU* 4.1 29.2 - - + -
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Residues in contact with HIS4884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4846D VAL* 5.2 10.9 + - + +
4849D TYR* 4.5 4.7 + - - +
4850D THR* 4.0 24.6 + - - +
4853D ALA* 3.7 21.3 - - + -
4861D TYR* 3.2 49.7 - + - -
4880D CYS* 2.9 33.3 + - + +
4881D TYR* 4.3 2.2 - - + +
4883D PHE* 1.3 86.9 - + + +
4885D MET* 1.3 59.0 + - - +
4888D GLY* 3.0 27.6 + - - +
4889D VAL* 4.1 2.1 + - - +
4895D ILE* 4.8 10.7 - - + +
4914D PHE* 6.2 0.7 - + - -
4918D PHE* 5.3 11.1 - + + -
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Residues in contact with MET4885 (chain D).
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* 4.1 17.0 - - + +
4920B PHE* 4.2 24.5 - - + -
4839D VAL* 6.5 0.4 - - + -
4842D LEU* 3.7 27.6 - - + -
4843D ALA* 6.0 1.8 - - + -
4846D VAL* 4.8 18.3 - - + +
4881D TYR* 3.1 33.5 + - + +
4882D LEU* 4.4 5.8 - - + +
4884D HIS* 1.3 76.5 - - - +
4886D TYR* 1.3 67.1 + - - +
4889D VAL* 3.3 38.0 + - + +
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Residues in contact with TYR4886 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4896B GLY* 4.0 12.8 - - - -
4899B ILE* 3.8 22.0 - - - +
4902B PRO* 5.1 15.2 - - + +
4911B ARG 4.8 1.8 + - - -
4912B VAL* 3.5 55.9 - - + -
4915B ASP* 3.6 26.9 - - + +
4916B ILE* 3.7 16.5 - - + +
4882D LEU* 3.1 19.9 + - + +
4883D PHE* 4.5 0.9 - - - +
4885D MET* 1.3 81.3 - - - +
4887D VAL* 1.3 77.6 + - + +
4890D ARG* 3.2 29.4 + - + +
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Residues in contact with VAL4887 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4883D PHE* 3.2 41.4 + - + +
4886D TYR* 1.3 95.2 - - + +
4888D GLY* 1.3 66.0 + - - +
4890D ARG* 5.0 1.1 - - - -
4891D ALA* 3.1 31.1 + - + +
4894D GLY 5.4 0.4 - - - +
4895D ILE* 5.5 3.4 - - + -
4897D ASP* 6.5 0.4 - - + -
4898D GLU* 4.1 24.7 - - + +
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Residues in contact with GLY4888 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4884D HIS* 3.0 20.1 + - - +
4887D VAL* 1.3 80.9 - - - +
4889D VAL* 1.3 62.9 + - - +
4891D ALA* 4.5 0.7 - - - +
4892D GLY* 3.6 14.9 + - - -
4894D GLY* 4.9 14.1 + - - +
4895D ILE* 4.8 14.1 - - - +
4918D PHE* 5.3 11.2 - - - -
4922D VAL* 6.4 1.6 - - - -
4923D ILE* 5.1 6.6 - - - +
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Residues in contact with VAL4889 (chain D).
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* 5.5 2.2 - - + -
4919B PHE* 3.2 23.0 - - + -
4920B PHE* 3.7 33.2 - - + -
4842D LEU* 5.0 11.4 - - + -
4846D VAL* 5.4 8.3 - - + -
4884D HIS 4.7 1.1 - - - +
4885D MET* 3.3 42.3 + - + +
4888D GLY* 1.3 76.1 - - - +
4890D ARG* 1.3 65.1 + - - +
4891D ALA 3.6 0.3 + - - -
4892D GLY* 3.7 7.1 + - - -
4922D VAL* 6.3 4.0 - - + -
4923D ILE* 6.3 1.1 - - - -
4927D LEU* 4.4 22.0 - - + +
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Residues in contact with ARG4890 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4893B GLY* 3.6 20.8 - - - +
4894B GLY* 5.9 0.7 - - - -
4896B GLY* 6.2 3.8 - - - +
4915B ASP* 5.5 2.2 - - + +
4916B ILE* 5.0 7.6 - - + +
4919B PHE* 3.5 40.8 - - + -
4885D MET 4.6 0.2 + - - -
4886D TYR* 3.2 26.3 + - + +
4887D VAL* 4.5 0.9 - - - +
4888D GLY 3.4 0.2 - - - -
4889D VAL* 1.3 77.5 - - - +
4891D ALA* 1.3 65.3 + - - +
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Residues in contact with ALA4891 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4893B GLY* 4.7 11.5 - - - -
4919B PHE* 5.8 0.2 - - - -
4887D VAL* 3.1 27.4 + - + +
4888D GLY 4.5 1.1 - - - +
4890D ARG* 1.3 79.8 - - - +
4892D GLY* 1.3 57.6 + - - +
4893D GLY* 3.2 12.2 + - - +
4894D GLY 4.9 7.9 - - - +
4897D ASP* 5.6 8.5 - - + -
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Residues in contact with GLY4892 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4919B PHE* 5.8 1.8 - - - -
4888D GLY 3.6 11.8 + - - -
4889D VAL 3.7 6.9 + - - -
4890D ARG 3.4 2.2 - - - -
4891D ALA* 1.3 77.7 - - - +
4893D GLY* 1.3 55.1 + - - +
4894D GLY 3.2 8.3 + - - -
4919D PHE* 4.2 5.7 - - - -
4923D ILE* 3.7 29.9 - - - +
4927D LEU* 6.0 4.0 - - - -
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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