Contacts of the helix formed by residues 4907 - 4922 (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 TYR4907 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4856D PHE* 4.7 36.9 - + + -
4857D PHE* 4.8 10.3 - + + -
4859D LYS* 5.9 5.4 - - - -
4860D PHE* 4.7 7.3 - + + -
4905D ASP 3.3 2.4 + - - -
4906D GLU* 1.3 77.8 - - + +
4908D GLU* 1.3 63.9 + - - +
4909D LEU 3.6 1.1 - - - -
4910D TYR* 3.9 31.0 - + + -
4911D ARG* 3.2 21.5 + - - +
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Residues in contact with GLU4908 (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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4860D PHE* 6.3 0.2 - - - -
4902D PRO* 5.3 11.6 - - - +
4904D GLY 3.4 22.0 - - - +
4905D ASP* 3.5 13.5 + - - +
4906D GLU 3.2 0.8 - - - -
4907D TYR* 1.3 78.6 - - - +
4909D LEU* 1.3 64.7 + - - +
4911D ARG* 3.4 3.2 + - - +
4912D VAL* 3.3 25.9 + - - +
4882F LEU* 6.3 0.2 - - - -
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Residues in contact with LEU4909 (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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4908D GLU* 1.3 77.7 - - - +
4910D TYR* 1.3 64.3 + - - +
4912D VAL* 3.4 9.3 + - - +
4913D VAL* 3.3 25.0 + - - +
4882F LEU* 5.4 10.3 - - + -
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Residues in contact with TYR4910 (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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4852D VAL* 5.9 1.9 - - - +
4856D PHE* 4.9 23.8 - + - -
4857D PHE* 3.7 30.1 - + - -
4907D TYR* 3.8 31.7 + + + +
4908D GLU 3.2 0.8 - - - -
4909D LEU* 1.3 79.5 - - - +
4911D ARG* 1.3 59.8 + - - +
4913D VAL* 3.3 22.8 - - + +
4914D PHE* 3.3 15.6 + + + +
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Residues in contact with ARG4911 (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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4857D PHE* 4.1 16.2 - - + -
4860D PHE* 4.1 23.6 - - + -
4902D PRO* 5.3 10.3 - - + -
4907D TYR 3.2 20.3 + - - +
4908D GLU* 3.9 3.8 - - - +
4910D TYR* 1.3 76.2 - - - +
4912D VAL* 1.3 64.9 + - - +
4914D PHE* 3.7 5.4 - - + +
4915D ASP* 3.3 22.2 + - - +
4886F TYR* 4.6 2.0 + - - -
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Residues in contact with VAL4912 (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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4902D PRO* 5.2 13.5 - - + -
4908D GLU 3.3 16.2 + - - +
4909D LEU* 3.7 9.2 - - - +
4910D TYR 3.3 0.6 - - - -
4911D ARG* 1.3 75.4 - - + +
4913D VAL* 1.3 67.1 + - - +
4915D ASP 3.4 1.7 + - - -
4916D ILE* 3.2 29.2 + - + +
4882F LEU* 3.8 39.0 - - + -
4886F TYR* 3.5 37.7 - - + -
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Residues in contact with VAL4913 (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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4909D LEU 3.3 12.7 + - - +
4910D TYR* 3.3 28.0 - - + +
4912D VAL* 1.3 82.4 - - + +
4914D PHE* 1.3 61.7 + - + +
4916D ILE* 3.3 9.7 + - + +
4917D THR* 3.2 27.1 + - + +
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Residues in contact with PHE4914 (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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4849D TYR* 3.5 46.0 - + + -
4852D VAL* 4.2 14.4 - - + -
4853D ALA* 5.3 0.7 - - + -
4857D PHE* 3.5 37.2 - + + -
4861D TYR* 4.4 16.6 - - - -
4884D HIS* 6.2 0.4 - + - -
4895D ILE* 4.5 15.0 - - + -
4899D ILE* 6.5 0.4 - - + -
4910D TYR* 3.3 18.5 + + + +
4911D ARG* 3.7 9.6 - - + +
4912D VAL 3.2 0.6 - - - -
4913D VAL* 1.3 82.4 - - - +
4915D ASP* 1.3 62.9 + - + +
4917D THR* 3.3 10.5 - - + +
4918D PHE* 3.1 34.9 + + + +
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Residues in contact with ASP4915 (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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4895D ILE* 4.1 22.9 + - + +
4896D GLY* 5.1 2.9 - - - +
4899D ILE* 5.6 1.6 - - + -
4911D ARG 3.3 8.9 + - - +
4914D PHE* 1.3 81.3 - - + +
4916D ILE* 1.3 61.6 + - - +
4918D PHE* 3.7 9.1 - - - +
4919D PHE* 3.0 28.6 + - - +
4886F TYR* 3.6 33.7 - - + +
4890F ARG* 5.5 1.8 - - - +
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Residues in contact with ILE4916 (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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4912D VAL* 3.2 21.7 + - + +
4913D VAL* 3.6 13.7 - - + +
4914D PHE 3.2 0.4 - - - -
4915D ASP* 1.3 78.3 - - - +
4917D THR* 1.3 64.1 + - - +
4919D PHE* 3.3 7.0 + - + +
4920D PHE* 3.1 51.3 + - + -
4885F MET* 4.1 20.9 - - + +
4886F TYR* 3.7 42.2 - - + +
4889F VAL* 5.5 1.6 - - + -
4890F ARG* 5.0 7.9 - - + +
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Residues in contact with THR4917 (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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4849D TYR* 3.6 18.1 + - + +
4913D VAL* 3.2 20.8 + - + +
4914D PHE* 3.3 15.0 - - + +
4916D ILE* 1.3 77.5 - - - +
4918D PHE* 1.3 64.5 + - - +
4920D PHE* 4.3 8.3 - - - -
4921D PHE* 3.1 47.5 + - - +
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Residues in contact with PHE4918 (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* 4.5 14.4 - - + -
4849D TYR* 3.8 41.1 - + + -
4884D HIS* 5.3 13.2 - - + -
4888D GLY* 5.3 7.4 - - - -
4894D GLY* 4.8 4.3 - - - -
4895D ILE* 3.7 51.8 - - + -
4914D PHE* 3.1 29.9 + + + +
4915D ASP* 3.7 7.4 - - - +
4916D ILE 3.2 0.2 - - - -
4917D THR* 1.3 79.1 - - - +
4919D PHE* 1.3 60.6 + - - +
4920D PHE 3.6 0.2 + - - -
4921D PHE* 5.2 0.4 - - - -
4922D VAL* 3.2 59.3 + - + +
4923D ILE* 3.6 0.8 - - + +
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Residues in contact with PHE4919 (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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4892D GLY 4.2 7.6 - - - -
4894D GLY* 4.5 11.2 - - - -
4915D ASP 3.0 18.1 + - - +
4916D ILE* 3.3 5.4 + - + +
4918D PHE* 1.3 77.1 - - - +
4920D PHE* 1.3 82.7 + + - +
4921D PHE 3.4 0.4 + - - -
4923D ILE* 3.4 42.2 - - + +
4924D VAL* 3.4 20.1 - - + +
4889F VAL* 3.2 38.6 - - + -
4890F ARG* 3.5 36.1 - - + -
4892F GLY* 5.7 2.0 - - - -
4927F LEU* 4.7 15.0 - - + -
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Residues in contact with PHE4920 (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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4916D ILE* 3.1 41.8 + - + +
4917D THR* 4.0 8.5 - - - +
4918D PHE 3.3 0.6 - - - -
4919D PHE* 1.3 104.5 - + - +
4921D PHE* 1.3 65.8 + - + +
4924D VAL* 3.2 28.8 - - + +
4925D ILE* 3.4 11.1 - - - +
4839F VAL* 6.2 5.6 - - + -
4842F LEU* 5.3 8.7 - - + -
4885F MET* 4.2 15.9 - - + -
4889F VAL* 3.7 24.2 - - + -
4927F LEU* 6.0 2.0 - - + -
4930F ILE* 6.1 4.8 - - + +
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Residues in contact with PHE4921 (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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4845D VAL* 6.6 0.2 - - + -
4849D TYR* 4.3 13.2 - - + +
4917D THR* 3.1 42.1 + - - +
4918D PHE* 4.6 0.9 - - - +
4919D PHE 3.4 0.2 - - - -
4920D PHE* 1.3 83.9 - - + +
4922D VAL* 1.3 70.2 + - + +
4923D ILE 3.3 0.7 - - - -
4925D ILE* 3.0 24.8 + - + +
4926D LEU* 2.9 24.3 + - - +
4828F VAL* 4.8 23.3 - - + -
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Residues in contact with VAL4922 (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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4842D LEU* 5.4 3.8 - - + +
4845D VAL* 4.0 30.1 - - + -
4846D VAL* 4.4 10.1 - - + -
4849D TYR* 4.9 4.9 - - + -
4888D GLY 6.4 1.6 - - - -
4889D VAL* 6.3 4.0 - - + -
4918D PHE* 3.2 49.3 + - + +
4921D PHE* 1.3 82.3 - - + +
4923D ILE* 1.3 71.2 + - + +
4926D LEU* 3.3 23.3 - - + +
4927D LEU* 3.4 16.8 - - - +
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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