Contacts of the helix formed by residues 4663 - 4681 (chain B) 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 LYS4663 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4659B TYR* 3.4 39.7 + - + +
4662B LEU* 1.3 84.5 - - + +
4664B VAL* 1.3 62.0 + - - +
4665B PRO 3.4 2.5 - - - -
4666B LEU* 2.9 15.6 + - + +
4667B VAL* 2.9 33.7 + - + +
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Residues in contact with VAL4664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4659B TYR* 3.2 36.3 + - + +
4660B ASN* 3.5 32.5 - - - +
4663B LYS* 1.3 76.1 - - - +
4665B PRO* 1.3 62.7 - - - +
4667B VAL* 3.2 7.6 - - + +
4668B ILE* 3.1 33.2 + - + +
4781B ILE* 3.6 40.8 - - + -
4787B PHE* 4.9 2.2 - - + -
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Residues in contact with PRO4665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4238B PHE* 3.2 37.0 - - + -
4660B ASN 3.3 20.9 - - - +
4661B CYS* 4.2 11.2 - - - +
4662B LEU 4.1 5.6 - - - +
4663B LYS 3.7 7.2 - - - +
4664B VAL* 1.3 89.2 - - + +
4666B LEU* 1.3 55.3 + - - +
4668B ILE* 4.0 5.9 - - + +
4669B PHE* 3.2 19.4 + - - +
4712B ASN* 4.4 7.2 - - - +
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Residues in contact with LEU4666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4235B ASP* 3.9 34.3 - - + +
4238B PHE* 4.5 6.5 - - + -
4239B GLU* 5.6 11.4 - - + -
4662B LEU 4.6 5.6 + - - +
4663B LYS* 2.9 24.8 + - + +
4665B PRO* 1.3 77.4 - - - +
4667B VAL* 1.3 65.0 + - + +
4668B ILE 3.2 0.2 - - - -
4669B PHE* 3.2 7.2 + - + -
4670B LYS* 2.7 34.8 + - + +
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Residues in contact with VAL4667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4659B TYR* 5.2 5.8 - - + +
4663B LYS* 2.9 17.7 + - + +
4664B VAL* 3.2 22.9 - - + +
4666B LEU* 1.3 78.8 - - + +
4668B ILE* 1.3 61.4 + - - +
4670B LYS* 3.9 8.6 - - + +
4671B ARG* 3.2 24.8 + - - +
4780B VAL* 5.6 6.3 - - + +
4781B ILE* 4.2 17.5 - - + -
4784B ASP* 5.8 6.7 - - + -
4786B SER* 4.7 14.8 - - - +
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Residues in contact with ILE4668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4664B VAL* 3.1 23.0 + - + +
4665B PRO* 4.2 5.8 - - + +
4667B VAL* 1.3 78.1 - - - +
4669B PHE* 1.3 57.9 + - - +
4671B ARG* 3.3 4.4 + - + +
4672B GLU* 2.8 30.7 + - + +
4710B PRO* 5.0 6.3 - - + -
4712B ASN* 3.8 27.4 - - + +
4773B TYR* 5.5 3.1 - - - +
4776B TRP* 4.7 26.0 - - + -
4777B LYS* 4.4 16.2 - - + +
4780B VAL* 4.9 9.9 - - + -
4781B ILE* 3.8 26.2 - - + -
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Residues in contact with PHE4669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4231B SER 5.6 0.7 - - - -
4234B GLU* 3.5 42.8 - - + -
4235B ASP* 4.1 11.7 - - + -
4238B PHE* 4.1 22.0 - + + -
4665B PRO 3.2 18.5 + - - +
4666B LEU* 3.8 4.9 - - + +
4668B ILE* 1.3 80.2 - - - +
4670B LYS* 1.3 60.2 + - - +
4672B GLU* 4.4 4.3 - - + +
4673B LYS* 3.0 36.4 + - + +
4712B ASN* 3.2 35.2 - - + -
4713B TYR* 3.8 29.6 - + + -
4714B TRP* 4.2 20.2 - + - -
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Residues in contact with LYS4670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4235B ASP* 6.5 0.2 - - + -
4666B LEU* 2.7 27.5 + - + +
4667B VAL* 3.9 10.1 - - - +
4668B ILE 3.3 0.2 - - - -
4669B PHE* 1.3 76.2 - - - +
4671B ARG* 1.3 60.0 + - - +
4673B LYS* 4.5 3.0 - - - +
4674B GLU* 3.8 17.2 + - - +
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Residues in contact with ARG4671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4667B VAL 3.2 16.0 + - - +
4668B ILE* 3.9 4.0 - - + +
4669B PHE 3.2 0.4 - - - -
4670B LYS* 1.3 75.5 - - - +
4672B GLU* 1.3 60.5 + - - +
4673B LYS 3.2 1.8 - - - -
4674B GLU* 3.3 6.6 + - + +
4675B LEU* 3.0 28.5 + - + +
4696B LYS* 4.1 29.7 + - - +
4700B ASP* 5.9 3.9 - - - +
4776B TRP* 3.9 29.4 - - + +
4780B VAL* 3.4 38.6 - - - +
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Residues in contact with GLU4672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4668B ILE* 2.8 28.6 + - + +
4669B PHE* 4.3 5.6 - - - +
4671B ARG* 1.3 73.7 - - - +
4673B LYS* 1.3 58.2 + - - +
4675B LEU* 3.8 9.4 - - + +
4676B ALA* 2.9 30.1 + - - +
4709B PHE* 6.3 2.2 - - + -
4710B PRO* 5.4 12.8 - - + +
4712B ASN* 5.6 1.8 - - + -
4713B TYR* 4.4 18.5 - - + +
4776B TRP* 5.1 10.7 - - + -
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Residues in contact with LYS4673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4231B SER* 5.3 8.7 - - - +
4669B PHE* 3.0 29.8 + - + +
4670B LYS* 4.5 3.8 - - - +
4672B GLU* 1.3 77.9 - - - +
4674B GLU* 1.3 58.0 + - - +
4676B ALA* 4.0 0.7 - - - +
4677B ARG* 3.0 29.5 + - - +
4713B TYR* 3.6 28.9 + - + -
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Residues in contact with GLU4674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4670B LYS 3.8 13.0 + - - +
4671B ARG* 3.3 12.0 + - + +
4673B LYS* 1.3 76.9 - - - +
4675B LEU* 1.3 60.2 + - - +
4677B ARG* 3.7 4.7 + - - +
4678B LYS* 3.0 27.4 + - - +
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Residues in contact with LEU4675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4671B ARG* 3.0 18.2 + - + +
4672B GLU* 3.8 8.3 - - + +
4673B LYS 3.3 0.2 - - - -
4674B GLU* 1.3 75.2 - - - +
4676B ALA* 1.3 64.3 + - - +
4678B LYS* 3.2 6.7 + - + +
4679B LEU* 3.2 33.0 + - + +
4684B LEU* 3.9 28.7 - - + -
4700B ASP* 4.6 14.6 - - + -
4703B VAL* 3.7 29.2 - - + -
4704B LEU* 4.7 5.4 - - + -
4709B PHE* 3.7 26.9 - - + -
4776B TRP* 4.9 8.1 - - + -
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Residues in contact with ALA4676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4672B GLU 2.9 19.3 + - - +
4673B LYS 4.0 0.9 - - - +
4675B LEU* 1.3 78.6 - - - +
4677B ARG* 1.3 60.3 + - - +
4679B LEU* 3.4 13.1 + - - +
4680B GLU* 3.7 9.2 + - - +
4709B PHE* 6.0 3.4 - - + -
4713B TYR* 4.0 34.3 - - + +
4718B VAL* 3.9 29.4 - - + +
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Residues in contact with ARG4677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4673B LYS 3.0 19.0 + - - +
4674B GLU* 4.1 4.7 - - - +
4676B ALA* 1.3 76.2 - - - +
4678B LYS* 1.3 61.5 + - - +
4679B LEU 3.3 0.2 - - - -
4680B GLU* 3.6 8.1 + - - +
4681B PHE* 3.4 20.1 + - - +
4713B TYR* 5.3 2.8 + - - +
5017B TRP* 6.4 2.0 - - + -
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Residues in contact with LYS4678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4674B GLU 3.0 19.7 + - - +
4675B LEU* 3.2 11.8 + - + +
4677B ARG* 1.3 75.0 - - - +
4679B LEU* 1.3 64.0 + - + +
4680B GLU 3.4 0.2 - - - -
4681B PHE* 2.8 27.8 - - - +
4682B ASP 3.4 7.0 - - - +
4683B GLY* 3.3 13.9 - - - -
4684B LEU* 5.5 4.0 - - + +
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Residues in contact with LEU4679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4675B LEU* 3.2 37.7 + - + +
4676B ALA* 3.7 10.1 - - - +
4677B ARG 3.3 0.4 - - - -
4678B LYS* 1.3 78.8 - - + +
4680B GLU* 1.3 64.2 + - - +
4681B PHE 3.2 6.8 - - - +
4683B GLY* 4.8 6.2 + - - -
4684B LEU* 4.5 12.8 - - + -
4686B ILE* 5.9 0.5 - - - +
4704B LEU* 5.1 7.0 - - + -
4709B PHE* 4.1 20.9 - - + -
4718B VAL* 4.0 29.8 - - + +
4719B LYS* 4.8 5.8 - - + -
4722B VAL* 3.7 37.5 - - + +
4726B HIS* 4.9 1.9 - - - -
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Residues in contact with GLU4680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4676B ALA 3.7 7.5 + - - +
4677B ARG* 3.6 10.6 + - - +
4678B LYS 3.4 0.4 - - - -
4679B LEU* 1.3 79.2 - - - +
4681B PHE* 1.3 60.0 + - - +
4718B VAL* 5.8 0.2 - - - +
4721B LYS* 6.4 2.5 - - + -
4722B VAL* 5.7 3.6 - - - +
4725B LYS* 5.3 6.3 - - - +
4726B HIS* 4.3 12.0 + - - -
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Residues in contact with PHE4681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4677B ARG 3.4 13.5 + - - +
4678B LYS* 2.8 14.7 - - - +
4679B LEU 3.2 10.1 - - - +
4680B GLU* 1.3 79.1 - - - +
4682B ASP* 1.3 66.3 + - - +
4683B GLY 3.0 2.8 + - - -
4726B HIS* 4.1 11.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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