Contacts of the helix formed by residues 4784 - 4799 (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 ASP4784 (chain D).
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Specific contacts
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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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Residues in contact with ASN4785 (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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4783D THR 3.6 2.4 + - - -
4784D ASP* 1.3 74.8 - - - +
4786D SER* 1.3 71.6 + - - +
4788D LEU* 4.0 5.5 - - - +
4789D TYR* 3.1 23.7 + - - +
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Residues in contact with SER4786 (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* 3.4 23.1 + - - -
4667D VAL* 4.7 11.6 - - - +
4784D ASP* 4.2 8.8 - - - +
4785D ASN* 1.3 85.7 + - - +
4787D PHE* 1.3 65.2 + - - +
4789D TYR* 3.4 13.1 + - - +
4790D LEU* 3.5 19.1 + - - +
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Residues in contact with PHE4787 (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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4656D ILE* 4.4 28.0 - - + -
4659D TYR* 4.0 31.1 + + + -
4660D ASN* 5.9 5.2 - - - -
4664D VAL* 4.9 3.8 - - + -
4781D ILE* 3.2 48.7 - - + +
4782D PHE* 4.0 28.3 - + - -
4784D ASP* 3.6 7.4 + - + +
4785D ASN 3.4 0.2 - - - -
4786D SER* 1.3 78.0 + - - +
4788D LEU* 1.3 63.3 + - - +
4790D LEU* 3.4 5.7 + - + +
4791D GLY* 2.9 29.6 + - - -
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Residues in contact with LEU4788 (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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4782D PHE 4.8 9.9 - - - +
4783D THR 5.6 0.7 - - - -
4784D ASP 3.0 20.5 + - - +
4785D ASN* 4.1 5.2 - - - +
4787D PHE* 1.3 78.4 - - - +
4789D TYR* 1.3 60.2 + - - +
4791D GLY* 3.8 2.2 - - - +
4792D TRP* 2.9 30.3 + - - +
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Residues in contact with TYR4789 (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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4561D ARG* 4.7 7.4 - - - -
4785D ASN 3.1 18.3 + - - +
4786D SER* 3.7 7.4 - - - +
4787D PHE 3.2 0.4 - - - -
4788D LEU* 1.3 79.2 - - - +
4790D LEU* 1.3 78.1 + - + +
4792D TRP* 3.5 18.5 + + + +
4793D TYR* 3.6 11.1 + - - +
4813D ASP* 2.7 39.0 + - + +
4816D MET* 3.9 18.6 - - + +
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Residues in contact with LEU4790 (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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4561D ARG* 3.5 34.3 - - - +
4655D CYS* 3.8 26.5 - - + -
4656D ILE* 5.3 9.3 - - + +
4659D TYR* 4.9 25.1 - - + -
4786D SER 3.5 10.9 + - - +
4787D PHE* 3.4 9.9 + - + +
4789D TYR* 1.3 98.4 - - + +
4791D GLY* 1.3 62.0 + - - +
4793D TYR* 3.4 15.8 + - + +
4794D MET* 3.7 9.9 + - - +
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Residues in contact with GLY4791 (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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4656D ILE* 5.9 5.6 - - - -
4787D PHE* 2.9 23.2 + - - -
4788D LEU* 3.8 2.7 - - - -
4789D TYR 3.3 0.2 - - - -
4790D LEU* 1.3 76.3 - - - +
4792D TRP* 1.3 62.8 + - - +
4794D MET* 3.2 17.1 + - - +
4795D VAL* 3.3 14.1 + - - +
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Residues in contact with TRP4792 (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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4788D LEU 2.9 18.6 + - - +
4789D TYR* 3.9 13.5 - + + +
4790D LEU 3.3 0.6 - - - -
4791D GLY* 1.3 76.7 - - - +
4793D TYR* 1.3 73.4 + + + +
4795D VAL* 3.2 25.9 - - + +
4796D MET* 3.6 17.1 + - + +
4809D ALA* 4.1 35.2 - - + -
4810D HIS* 5.8 1.3 - + - -
4812D LEU* 6.0 3.4 - - + -
4813D ASP* 5.9 4.0 - - + -
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Residues in contact with TYR4793 (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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4561D ARG* 4.6 11.0 - - - +
4564D ALA* 3.8 29.3 + - + +
4568D ALA* 5.1 0.9 - - - +
4648D HIS* 2.4 46.3 + + - -
4651D VAL* 6.6 0.2 - - + -
4652D ALA* 4.3 19.5 - - + -
4789D TYR 3.6 8.0 + - - +
4790D LEU* 3.4 13.2 + - + +
4791D GLY 3.2 0.8 - - - -
4792D TRP* 1.3 90.0 - + + +
4794D MET* 1.3 50.0 + - - +
4796D MET* 4.2 2.0 - - - -
4797D SER* 2.6 28.9 + - - -
4810D HIS* 3.4 37.3 + + + +
4813D ASP* 3.2 38.4 - - + +
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Residues in contact with MET4794 (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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4652D ALA* 4.9 11.2 - - + +
4653D PHE* 5.8 0.9 - - + -
4656D ILE* 3.9 28.0 - - + -
4790D LEU 3.7 7.2 + - - +
4791D GLY* 3.2 11.2 + - - +
4793D TYR* 1.3 77.7 - - - +
4795D VAL* 1.3 65.2 + - - +
4796D MET 3.3 1.6 - - - -
4797D SER* 3.2 21.3 + - - -
4798D LEU* 3.7 9.4 + - - +
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Residues in contact with VAL4795 (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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4791D GLY 3.3 11.6 + - - +
4792D TRP* 3.2 34.5 - - + +
4794D MET* 1.3 77.7 - - - +
4796D MET* 1.3 61.6 + - + +
4797D SER 3.5 0.3 + - - -
4798D LEU* 3.6 11.5 + - - +
4799D LEU* 3.4 23.0 - - + +
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Residues in contact with MET4796 (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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4792D TRP* 3.6 25.3 + - + +
4793D TYR* 4.4 1.6 - - - +
4794D MET 3.3 0.4 - - - -
4795D VAL* 1.3 80.6 - - + +
4797D SER* 1.3 63.9 + - - +
4798D LEU 3.3 0.4 - - - -
4799D LEU* 3.3 21.6 + - + +
4800D GLY* 3.6 7.1 + - - -
4806D PHE* 4.7 12.0 - - + +
4809D ALA* 5.3 7.0 - - + -
4810D HIS* 3.8 25.6 + - + +
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Residues in contact with SER4797 (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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4648D HIS* 4.3 10.4 - - - -
4649D THR* 3.6 36.4 - - - +
4652D ALA* 4.1 11.2 - - - +
4793D TYR 2.6 25.1 + - - -
4794D MET* 3.2 12.6 + - - -
4796D MET* 1.3 78.3 - - - +
4798D LEU* 1.3 62.9 + - - +
4800D GLY* 3.3 10.7 + - - -
4801D HIS* 3.8 5.4 - - - -
4807D PHE* 5.6 0.7 - - - -
4810D HIS* 4.1 12.5 + - - -
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Residues in contact with LEU4798 (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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4649D THR* 5.3 5.8 - - + -
4794D MET 3.7 8.2 + - - +
4795D VAL* 3.6 11.1 + - - +
4796D MET 3.3 0.6 - - - -
4797D SER* 1.3 79.5 - - - +
4799D LEU* 1.3 64.9 + - + +
4800D GLY 3.3 0.7 + - - -
4801D HIS* 3.6 26.9 + - + +
4802D TYR* 4.4 2.1 + - - +
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Residues in contact with LEU4799 (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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4795D VAL* 3.4 24.9 - - + +
4796D MET* 3.3 12.5 + - + +
4797D SER 3.2 0.8 - - - -
4798D LEU* 1.3 80.1 - - + +
4800D GLY* 1.3 63.0 + - - +
4801D HIS 3.3 0.4 - - - -
4802D TYR* 3.2 25.1 + - + +
4804D ASN 3.6 8.8 - - - +
4806D PHE* 4.1 46.5 - - + -
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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