Contacts of the helix formed by residues 4770 - 4784 (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 ASP4770 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4706H THR* 5.4 4.9 - - + -
4707H PRO* 5.6 6.7 - - + -
4768H SER 3.7 3.5 + - - +
4769H ILE* 1.3 76.1 - - - +
4771H VAL* 1.3 60.0 + - - +
4772H LYS* 4.3 3.4 - - + +
4773H TYR* 3.9 27.1 - - + +
4774H GLN* 2.9 31.8 + - - +
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Residues in contact with VAL4771 (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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4769H ILE 4.4 0.6 + - - -
4770H ASP* 1.3 73.0 - - - +
4772H LYS* 1.3 76.7 + - + +
4774H GLN* 4.2 5.0 - - - +
4775H ILE* 3.4 23.5 + - + +
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Residues in contact with LYS4772 (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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4702H LEU* 3.6 17.2 - - - +
4705H ASN* 3.5 57.1 + - - +
4706H THR* 4.2 11.6 + - + +
4707H PRO* 4.9 7.2 - - + +
4770H ASP* 3.2 3.2 - - + +
4771H VAL* 1.3 89.1 - - + +
4773H TYR* 1.3 59.6 + - - +
4775H ILE* 3.9 3.4 + - - +
4776H TRP* 3.7 15.9 + - - +
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Residues in contact with TYR4773 (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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4668H ILE* 5.5 3.7 - - + +
4703H VAL* 5.7 2.2 - - + -
4706H THR* 4.2 21.5 + - + -
4708H SER 5.5 1.1 - - - -
4710H PRO* 3.6 38.3 - - + +
4712H ASN* 4.8 5.9 + - - -
4770H ASP* 3.4 23.9 + - + +
4771H VAL 3.3 0.4 - - - -
4772H LYS* 1.3 79.2 - - - +
4774H GLN* 1.3 63.4 + - + +
4775H ILE 3.2 0.7 - - - -
4776H TRP* 3.5 9.8 + + - -
4777H LYS* 2.9 51.6 + - + +
4778H PHE* 6.4 2.0 - + - -
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Residues in contact with GLN4774 (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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4769H ILE* 6.3 1.6 - - + -
4770H ASP 2.9 19.2 + - - +
4771H VAL* 4.2 5.6 - - - +
4772H LYS 3.5 0.2 - - - -
4773H TYR* 1.3 82.0 - - + +
4775H ILE* 1.3 61.8 + - - +
4777H LYS* 4.8 1.8 - - - -
4778H PHE* 3.3 50.1 + - + +
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Residues in contact with ILE4775 (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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4699H TRP* 3.5 19.4 - - + -
4702H LEU* 5.2 7.4 - - + -
4771H VAL* 3.4 15.1 + - + +
4772H LYS* 4.3 4.5 - - - +
4773H TYR 3.2 0.4 - - - -
4774H GLN* 1.3 79.9 - - - +
4776H TRP* 1.3 58.1 + - - +
4778H PHE* 5.4 0.4 - - - -
4779H GLY* 3.1 19.9 + - - -
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Residues in contact with TRP4776 (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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4668H ILE* 4.7 19.1 - - + -
4671H ARG* 3.9 32.1 - - + +
4672H GLU* 5.1 14.6 - - + -
4675H LEU* 4.9 8.1 - - + -
4699H TRP* 3.3 38.0 + + - +
4700H ASP* 3.6 13.6 - - + +
4702H LEU* 3.9 14.5 - - + +
4703H VAL* 3.5 49.5 - - + +
4710H PRO* 4.3 22.2 - - + -
4772H LYS 3.7 10.1 + - - +
4773H TYR* 3.5 10.4 + + - +
4774H GLN 3.5 0.2 - - - -
4775H ILE* 1.3 77.4 - - - +
4777H LYS* 1.3 78.6 + - + +
4779H GLY 3.6 0.2 + - - -
4780H VAL* 3.3 27.3 + - + +
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Residues in contact with LYS4777 (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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4668H ILE* 4.4 9.7 - - + +
4773H TYR* 2.9 48.8 + - + +
4774H GLN* 4.6 1.6 - - - +
4776H TRP* 1.3 90.1 - - + +
4778H PHE* 1.3 74.3 + - + +
4779H GLY 3.3 0.9 + - - -
4780H VAL* 3.4 6.1 + - - +
4781H ILE* 3.2 22.2 + - - +
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Residues in contact with PHE4778 (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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4660H ASN* 6.3 1.8 - - - -
4773H TYR* 6.4 2.0 - + - -
4774H GLN* 3.3 37.5 + - + +
4777H LYS* 1.3 84.2 - - + +
4779H GLY* 1.3 61.9 + - - +
4780H VAL 3.4 0.2 - - - -
4781H ILE* 3.9 10.3 - - + +
4782H PHE* 3.2 51.5 + + + -
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Residues in contact with GLY4779 (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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4699H TRP* 3.6 22.7 - - - -
4775H ILE 3.1 22.2 + - - -
4777H LYS 3.2 0.6 - - - -
4778H PHE* 1.3 78.2 - - - +
4780H VAL* 1.3 59.2 + - - +
4782H PHE* 3.6 4.8 + - - +
4783H THR* 2.8 32.9 + - - +
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Residues in contact with VAL4780 (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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4667H VAL* 5.6 7.0 - - + +
4668H ILE* 4.9 7.4 - - + -
4671H ARG* 3.4 49.1 - - + +
4699H TRP* 4.3 14.6 - - + -
4776H TRP* 3.3 25.1 - - + +
4777H LYS* 3.4 5.7 + - - +
4778H PHE 3.4 0.4 - - - -
4779H GLY* 1.3 74.8 - - - +
4781H ILE* 1.3 66.7 + - + +
4783H THR* 3.2 7.5 + - - +
4784H ASP* 2.9 31.8 + - + +
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Residues in contact with ILE4781 (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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4660H ASN* 6.2 1.1 - - - +
4664H VAL* 3.6 34.1 - - + -
4667H VAL* 4.2 12.6 - - + -
4668H ILE* 3.8 25.1 - - + -
4777H LYS 3.2 16.8 - - - +
4778H PHE* 3.5 11.8 + - + +
4779H GLY 3.3 0.6 - - - -
4780H VAL* 1.3 82.7 - - + +
4782H PHE* 1.3 66.3 + - + +
4784H ASP* 3.4 10.5 + - + +
4787H PHE* 3.2 62.0 - - + +
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Residues in contact with PHE4782 (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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4778H PHE* 3.2 39.8 + + + +
4779H GLY* 4.2 5.4 - - - +
4780H VAL 3.4 0.2 - - - -
4781H ILE* 1.3 81.2 - - + +
4783H THR* 1.3 61.2 + - + +
4784H ASP 3.4 3.1 + - - +
4787H PHE* 4.0 27.2 - + - -
4788H LEU* 4.8 9.0 - - - +
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Residues in contact with THR4783 (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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4699H TRP* 6.2 4.7 - - + -
4779H GLY* 2.8 23.1 + - - +
4780H VAL* 3.2 12.0 + - - +
4782H PHE* 1.3 80.4 - - + +
4784H ASP* 1.3 64.0 + - - +
4785H ASN* 3.6 1.7 + - - -
4788H LEU* 5.6 0.7 - - - -
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Residues in contact with ASP4784 (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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4667H VAL* 5.8 8.1 - - + -
4780H VAL* 2.9 22.1 + - + +
4781H ILE* 3.4 14.5 + - + +
4783H THR* 1.3 77.1 - - - +
4785H ASN* 1.3 61.6 + - - +
4786H SER* 3.3 14.4 - - - +
4787H PHE* 4.2 7.4 - - + +
4788H LEU* 3.0 30.9 + - - +
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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