Contacts of the helix formed by residues 4784 - 4799 (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 ASP4784 (chain H).
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Specific contacts
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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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Residues in contact with ASN4785 (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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4783H THR 3.6 3.0 + - - -
4784H ASP* 1.3 75.6 - - - +
4786H SER* 1.3 70.2 + - - +
4788H LEU* 4.0 4.7 - - - +
4789H TYR* 3.1 23.9 + - - +
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Residues in contact with SER4786 (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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4659H TYR* 3.4 22.0 + - - -
4667H VAL* 4.7 11.4 - - - +
4784H ASP* 4.2 9.4 - - - +
4785H ASN* 1.3 84.0 + - - +
4787H PHE* 1.3 64.2 + - - +
4789H TYR* 3.4 13.8 + - - +
4790H LEU* 3.5 19.2 + - - +
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Residues in contact with PHE4787 (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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4656H ILE* 4.4 27.4 - - + -
4659H TYR* 4.0 32.3 + + + -
4660H ASN* 5.9 4.5 - - + -
4664H VAL* 4.9 3.8 - - + -
4781H ILE* 3.2 47.6 - - + +
4782H PHE* 4.0 29.4 - + - -
4784H ASP* 3.6 7.0 + - + +
4785H ASN 3.4 0.2 - - - -
4786H SER* 1.3 78.7 + - - +
4788H LEU* 1.3 62.5 + - - +
4790H LEU* 3.4 6.2 + - + +
4791H GLY* 2.9 28.4 + - - -
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Residues in contact with LEU4788 (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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4781H ILE 4.9 0.2 + - - -
4782H PHE 4.8 9.4 - - - +
4783H THR 5.6 0.4 - - - -
4784H ASP 3.0 19.7 + - - +
4785H ASN* 4.1 6.1 - - - +
4787H PHE* 1.3 77.7 - - - +
4789H TYR* 1.3 60.4 + - - +
4791H GLY* 4.4 2.2 - - - +
4792H TRP* 2.9 30.0 + - - +
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Residues in contact with TYR4789 (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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4561H ARG* 4.7 7.2 - - - -
4785H ASN 3.1 18.3 + - - +
4786H SER* 3.7 6.5 - - - +
4787H PHE 3.2 0.4 - - - -
4788H LEU* 1.3 79.0 - - - +
4790H LEU* 1.3 78.6 + - + +
4792H TRP* 3.5 19.1 + + + +
4793H TYR* 3.6 11.1 + - - +
4813H ASP* 2.7 39.5 + - + +
4816H MET* 3.9 18.2 - - + +
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Residues in contact with LEU4790 (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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4561H ARG* 3.5 33.4 - - - +
4655H CYS* 3.8 27.1 - - + -
4656H ILE* 5.3 9.6 - - + +
4659H TYR* 4.9 24.7 - - + -
4786H SER 3.5 12.0 + - - +
4787H PHE* 3.4 9.7 + - + +
4789H TYR* 1.3 99.5 - - + +
4791H GLY* 1.3 61.7 + - - +
4793H TYR* 3.4 16.9 + - + +
4794H MET* 3.7 9.5 + - - +
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Residues in contact with GLY4791 (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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4656H ILE* 5.9 5.4 - - - -
4787H PHE* 2.9 22.6 + - - -
4788H LEU* 3.8 2.9 - - - -
4789H TYR 3.3 0.2 - - - -
4790H LEU* 1.3 76.5 - - - +
4792H TRP* 1.3 62.0 + - - +
4794H MET* 3.2 16.4 + - - +
4795H VAL* 3.3 14.6 + - - +
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Residues in contact with TRP4792 (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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4788H LEU 2.9 17.7 + - - +
4789H TYR* 3.9 14.4 - + + +
4790H LEU 3.3 0.4 - - - -
4791H GLY* 1.3 77.6 - - - +
4793H TYR* 1.3 73.2 + + + +
4795H VAL* 3.2 25.5 - - + +
4796H MET* 3.6 16.6 + - + +
4809H ALA* 4.1 36.3 - - + -
4810H HIS* 5.8 1.1 - + - -
4812H LEU* 6.0 3.1 - - + -
4813H ASP* 5.9 3.8 - - + -
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Residues in contact with TYR4793 (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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4561H ARG* 4.6 10.5 - - - +
4564H ALA* 3.8 30.3 + - + +
4568H ALA* 5.1 0.7 - - - +
4648H HIS* 2.4 44.7 + + - -
4651H VAL* 6.6 0.2 - - + -
4652H ALA* 4.3 19.7 - - + -
4789H TYR 3.6 8.2 + - - +
4790H LEU* 3.4 12.7 + - + +
4791H GLY 3.2 0.8 - - - -
4792H TRP* 1.3 90.0 - + + +
4794H MET* 1.3 49.3 + - - +
4795H VAL 3.6 0.2 - - - -
4796H MET* 4.1 2.1 + - - -
4797H SER* 2.6 29.5 + - - -
4810H HIS* 3.4 38.3 + + + +
4813H ASP* 3.2 38.1 - - + +
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Residues in contact with MET4794 (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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4652H ALA* 4.9 11.7 - - + +
4653H PHE* 5.8 0.4 - - + -
4656H ILE* 3.9 28.0 - - + -
4790H LEU 3.7 6.4 + - - +
4791H GLY* 3.2 11.2 + - - +
4793H TYR* 1.3 77.5 - - - +
4795H VAL* 1.3 64.3 + - - +
4796H MET 3.3 1.6 - - - -
4797H SER* 3.2 20.4 + - - -
4798H LEU* 3.7 9.4 + - - +
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Residues in contact with VAL4795 (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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4791H GLY 3.3 11.5 + - - +
4792H TRP* 3.2 34.3 - - + +
4794H MET* 1.3 78.9 - - - +
4796H MET* 1.3 61.0 + - + +
4797H SER 3.5 0.3 + - - -
4798H LEU* 3.6 12.2 + - - +
4799H LEU* 3.4 22.4 - - + +
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Residues in contact with MET4796 (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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4792H TRP* 3.6 25.9 + - + +
4793H TYR* 4.4 1.3 - - - +
4794H MET 3.3 0.4 - - - -
4795H VAL* 1.3 79.8 - - + +
4797H SER* 1.3 63.7 + - - +
4799H LEU* 3.3 21.4 + - + +
4800H GLY* 3.6 7.1 + - - -
4806H PHE* 4.7 11.7 - - + +
4809H ALA* 5.3 6.5 - - + -
4810H HIS* 3.8 27.3 + - + +
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Residues in contact with SER4797 (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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4648H HIS* 4.3 10.5 - - - -
4649H THR* 3.6 36.5 - - - +
4652H ALA* 4.1 10.5 - - - +
4793H TYR 2.6 25.3 + - - -
4794H MET* 3.2 13.4 + - - -
4796H MET* 1.3 78.9 - - - +
4798H LEU* 1.3 62.1 + - - +
4800H GLY* 3.3 11.3 + - - -
4801H HIS* 3.8 5.7 - - - -
4807H PHE* 5.6 0.7 - - - -
4810H HIS* 4.1 12.6 + - - -
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Residues in contact with LEU4798 (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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4649H THR* 5.3 5.6 - - + -
4794H MET 3.7 8.2 + - - +
4795H VAL* 3.6 10.4 + - - +
4796H MET 3.3 0.6 - - - -
4797H SER* 1.3 80.0 - - - +
4799H LEU* 1.3 65.5 + - + +
4800H GLY 3.3 0.7 + - - -
4801H HIS* 3.6 27.7 + - + +
4802H TYR* 4.4 1.4 + - - +
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Residues in contact with LEU4799 (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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4795H VAL* 3.4 24.7 - - + +
4796H MET* 3.3 11.9 + - - +
4797H SER 3.2 0.8 - - - -
4798H LEU* 1.3 79.6 - - + +
4800H GLY* 1.3 63.2 + - - +
4801H HIS 3.3 0.4 - - - -
4802H TYR* 3.2 24.5 + - + +
4804H ASN 3.6 9.0 - - - +
4806H PHE* 4.1 45.2 - - + -
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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