Contacts of the helix formed by residues 4770 - 4784 (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 ASP4770 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4706D THR* 5.4 5.2 - - + -
4707D PRO* 5.6 6.5 - - + -
4768D SER 3.7 3.7 + - - +
4769D ILE* 1.3 77.1 - - - +
4771D VAL* 1.3 61.2 + - - +
4772D LYS* 4.3 3.1 - - + +
4773D TYR* 3.8 26.7 - - + +
4774D GLN* 2.9 32.2 + - - +
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Residues in contact with VAL4771 (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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4769D ILE 4.4 0.6 + - - -
4770D ASP* 1.3 73.2 - - - +
4772D LYS* 1.3 75.6 + - + +
4774D GLN* 4.2 5.1 - - - +
4775D ILE* 3.4 23.1 + - + +
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Residues in contact with LYS4772 (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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4702D LEU* 3.6 16.2 - - - +
4705D ASN* 3.5 56.7 + - - +
4706D THR* 4.2 11.8 + - + +
4707D PRO* 4.9 7.2 - - + +
4770D ASP* 3.2 3.5 - - + +
4771D VAL* 1.3 90.2 - - + +
4773D TYR* 1.3 59.1 + - - +
4775D ILE* 3.9 3.5 + - - +
4776D TRP* 3.7 15.9 + - - +
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Residues in contact with TYR4773 (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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4668D ILE* 5.5 3.2 - - + +
4703D VAL* 5.7 2.0 - - + -
4706D THR* 4.2 22.1 + - + +
4708D SER 5.5 1.3 - - - -
4710D PRO* 3.6 38.2 - - + +
4712D ASN* 4.8 6.1 + - - -
4770D ASP* 3.4 24.3 + - + +
4771D VAL 3.3 0.2 - - - -
4772D LYS* 1.3 78.3 - - - +
4774D GLN* 1.3 63.2 + - - +
4775D ILE 3.2 0.7 - - - -
4776D TRP* 4.1 10.7 - + - +
4777D LYS* 2.9 52.3 + - + +
4778D PHE* 6.4 2.0 - + - -
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Residues in contact with GLN4774 (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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4769D ILE* 6.3 2.2 - - + -
4770D ASP 2.9 18.8 + - - +
4771D VAL* 3.7 6.3 + - - +
4772D LYS 3.5 0.2 - - - -
4773D TYR* 1.3 81.6 - - + +
4775D ILE* 1.3 61.4 + - - +
4777D LYS* 4.8 1.3 - - - -
4778D PHE* 3.3 49.6 + - + +
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Residues in contact with ILE4775 (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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4699D TRP* 3.5 20.0 - - + -
4702D LEU* 5.2 7.2 - - + -
4771D VAL* 3.4 16.1 + - + +
4772D LYS* 4.3 4.3 - - - +
4773D TYR 3.2 1.0 - - - -
4774D GLN* 1.3 80.3 - - - +
4776D TRP* 1.3 57.9 + - - +
4779D GLY* 3.1 20.1 + - - -
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Residues in contact with TRP4776 (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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4668D ILE* 4.7 19.3 - - + -
4671D ARG* 3.9 31.7 - - + +
4672D GLU* 5.1 14.4 - - + -
4675D LEU* 4.9 8.1 - - + -
4699D TRP* 3.3 38.5 + + - +
4700D ASP* 3.6 14.0 - - + +
4702D LEU* 3.9 13.9 - - + +
4703D VAL* 3.5 48.0 - - + +
4710D PRO* 4.3 22.0 - - + -
4772D LYS 3.7 10.3 + - - +
4773D TYR* 3.5 10.6 + + - +
4774D GLN 3.5 0.2 - - - -
4775D ILE* 1.3 78.5 - - - +
4777D LYS* 1.3 79.3 + - + +
4779D GLY 3.6 0.2 + - - -
4780D VAL* 3.3 27.5 + - + +
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Residues in contact with LYS4777 (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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4668D ILE* 4.4 10.1 - - + +
4773D TYR* 2.9 48.4 + - + +
4774D GLN* 4.6 1.3 - - - +
4776D TRP* 1.3 89.8 - - + +
4778D PHE* 1.3 73.6 + - + +
4779D GLY 3.3 0.5 + - - -
4780D VAL* 3.4 6.1 + - - +
4781D ILE* 3.2 22.4 + - - +
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Residues in contact with PHE4778 (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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4660D ASN* 6.3 1.3 - - - -
4773D TYR* 6.4 2.2 - + - -
4774D GLN* 3.3 37.0 + - + +
4777D LYS* 1.3 84.0 - - + +
4779D GLY* 1.3 60.9 + - - +
4780D VAL 3.4 0.2 - - - -
4781D ILE* 3.9 10.7 - - + +
4782D PHE* 3.2 52.6 + + + -
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Residues in contact with GLY4779 (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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4699D TRP* 3.6 22.2 - - - -
4775D ILE 3.1 21.8 + - - -
4776D TRP 3.6 0.2 + - - -
4777D LYS 3.2 0.6 - - - -
4778D PHE* 1.3 79.1 - - - +
4780D VAL* 1.3 59.2 + - - +
4782D PHE* 3.6 5.5 + - - +
4783D THR* 2.8 32.7 + - - +
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Residues in contact with VAL4780 (chain D).
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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4667D VAL* 5.6 7.2 - - + +
4668D ILE* 4.9 7.0 - - + -
4671D ARG* 3.4 48.7 - - + +
4699D TRP* 4.3 15.0 - - + -
4776D TRP* 3.3 24.7 - - + +
4777D LYS* 3.4 6.1 + - - +
4778D PHE 3.4 0.4 - - - -
4779D GLY* 1.3 75.0 - - - +
4781D ILE* 1.3 69.3 + - + +
4783D THR* 3.2 8.1 + - - +
4784D ASP* 2.9 31.7 + - + +
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Residues in contact with ILE4781 (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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4659D TYR* 6.0 0.2 - - + -
4660D ASN* 6.2 1.1 - - - +
4664D VAL* 3.6 35.9 - - + -
4667D VAL* 4.2 13.2 - - + -
4668D ILE* 3.8 24.7 - - + -
4777D LYS 3.2 16.8 - - - +
4778D PHE* 4.1 12.1 - - + +
4779D GLY 3.3 0.6 - - - -
4780D VAL* 1.3 82.2 - - + +
4782D PHE* 1.3 65.8 + - + +
4784D ASP* 3.4 9.1 + - + +
4787D PHE* 3.2 61.4 - - + +
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Residues in contact with PHE4782 (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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4778D PHE* 3.2 40.1 + + + +
4779D GLY* 4.2 5.2 - - - +
4780D VAL 3.4 0.2 - - - -
4781D ILE* 1.3 81.0 - - + +
4783D THR* 1.3 61.5 + - + +
4784D ASP 3.4 3.2 - - - +
4787D PHE* 4.0 27.2 - + - -
4788D LEU* 4.8 8.7 - - - +
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Residues in contact with THR4783 (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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4699D TRP* 6.2 5.2 - - + -
4779D GLY* 2.8 22.7 + - - +
4780D VAL* 3.2 12.1 + - - +
4782D PHE* 1.3 80.8 - - + +
4784D ASP* 1.3 65.1 + - - +
4785D ASN* 3.6 2.1 + - - -
4788D LEU* 5.6 0.4 - - - -
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Residues in contact with ASP4784 (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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4667D VAL* 5.8 8.5 - - + -
4780D VAL* 2.9 21.0 + - + +
4781D ILE* 3.4 15.0 + - + +
4782D PHE 4.5 0.2 - - - +
4783D THR* 1.3 77.8 - - - +
4785D ASN* 1.3 61.2 + - - +
4786D SER* 4.2 14.4 - - - +
4787D PHE* 4.1 7.4 - - + +
4788D LEU* 3.0 31.2 + - - +
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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