Contacts of the helix formed by residues 4663 - 4681 (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 LYS4663 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4659H TYR* 3.4 39.4 + - + +
4662H LEU* 1.3 84.5 - - + +
4664H VAL* 1.3 62.2 + - - +
4665H PRO 3.4 1.8 - - - -
4666H LEU* 2.9 16.6 + - + +
4667H VAL* 2.9 33.2 + - + +
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Residues in contact with VAL4664 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4659H TYR* 3.2 35.4 - - + +
4660H ASN* 3.5 31.2 - - - +
4663H LYS* 1.3 75.9 - - - +
4665H PRO* 1.3 63.3 - - + +
4667H VAL* 3.2 7.7 - - + +
4668H ILE* 3.1 33.7 + - + +
4781H ILE* 3.6 42.0 - - + -
4787H PHE* 4.9 2.5 - - + -
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Residues in contact with PRO4665 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4238H PHE* 3.2 36.6 - - + -
4660H ASN 3.3 19.7 - - - +
4661H CYS* 4.4 10.1 - - - +
4662H LEU 4.1 5.6 - - - +
4663H LYS 3.7 7.9 - - - +
4664H VAL* 1.3 89.7 - - + +
4666H LEU* 1.3 56.1 + - - +
4668H ILE* 4.0 6.5 - - + +
4669H PHE* 3.2 19.4 + - - +
4712H ASN* 4.4 7.7 - - - +
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Residues in contact with LEU4666 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4235H ASP* 3.9 33.4 - - + +
4238H PHE* 4.5 6.7 - - + -
4239H GLU* 5.6 11.2 - - + -
4662H LEU 4.6 5.8 + - - +
4663H LYS* 2.9 24.4 + - + +
4665H PRO* 1.3 78.6 - - - +
4667H VAL* 1.3 65.7 + - + +
4669H PHE* 3.2 7.0 + - + -
4670H LYS* 2.7 34.3 + - + +
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Residues in contact with VAL4667 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4659H TYR* 5.2 5.6 - - + +
4663H LYS* 2.9 17.1 + - + +
4664H VAL* 3.2 22.2 - - + +
4666H LEU* 1.3 78.8 - - + +
4668H ILE* 1.3 61.4 + - - +
4670H LYS* 3.9 9.0 - - + +
4671H ARG* 3.2 23.9 + - - +
4780H VAL* 5.6 6.6 - - + +
4781H ILE* 4.2 18.4 - - + -
4784H ASP* 5.8 7.2 - - + -
4786H SER* 4.7 14.6 - - - +
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Residues in contact with ILE4668 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4664H VAL* 3.1 23.6 + - + +
4665H PRO* 4.1 5.6 - - + +
4667H VAL* 1.3 79.0 - - - +
4669H PHE* 1.3 57.9 + - - +
4671H ARG* 3.3 3.7 + - + +
4672H GLU* 2.8 30.4 + - + +
4710H PRO* 5.0 5.4 - - + -
4712H ASN* 3.8 27.6 - - + +
4773H TYR* 5.5 3.6 - - - +
4776H TRP* 4.7 26.4 - - + -
4777H LYS* 4.4 16.4 - - + +
4780H VAL* 4.9 9.9 - - + -
4781H ILE* 3.8 26.7 - - + -
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Residues in contact with PHE4669 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4231H SER 5.6 0.7 - - - -
4234H GLU* 3.5 42.0 - - + -
4235H ASP* 4.1 11.4 - - + -
4238H PHE* 4.1 22.2 - + + -
4665H PRO 3.2 18.3 + - - +
4666H LEU* 3.2 6.2 + - + +
4668H ILE* 1.3 80.7 - - - +
4670H LYS* 1.3 60.4 + - - +
4672H GLU* 4.4 4.3 - - + +
4673H LYS* 3.0 36.6 + - + +
4712H ASN* 3.2 35.7 - - + -
4713H TYR* 3.8 30.1 - + + -
4714H TRP* 4.2 20.0 - + - -
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Residues in contact with LYS4670 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4235H ASP* 6.5 0.4 - - + -
4666H LEU* 2.7 27.6 + - + +
4667H VAL* 3.9 10.5 - - + +
4668H ILE 3.3 0.4 - - - -
4669H PHE* 1.3 76.2 - - - +
4671H ARG* 1.3 58.9 + - - +
4673H LYS* 4.5 2.8 - - - +
4674H GLU* 3.8 16.6 + - - +
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Residues in contact with ARG4671 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4667H VAL 3.2 16.0 + - - +
4668H ILE* 3.9 4.9 - - + +
4669H PHE 3.2 0.2 - - - -
4670H LYS* 1.3 76.7 - - - +
4672H GLU* 1.3 59.3 + - - +
4673H LYS 3.2 1.6 - - - -
4674H GLU* 3.3 6.3 + - + +
4675H LEU* 3.0 28.5 + - + +
4696H LYS* 4.1 30.3 + - - +
4700H ASP* 5.9 4.5 - - - +
4776H TRP* 3.9 28.5 - - + +
4780H VAL* 3.4 39.6 - - - +
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Residues in contact with GLU4672 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4668H ILE* 2.8 27.7 + - + +
4669H PHE* 4.3 5.4 - - - +
4671H ARG* 1.3 73.3 - - - +
4673H LYS* 1.3 57.0 + - - +
4675H LEU* 3.4 8.4 + - + +
4676H ALA* 2.9 30.7 + - - +
4709H PHE* 6.3 2.0 - - + -
4710H PRO* 5.4 13.0 - - + +
4712H ASN* 5.6 2.0 - - + -
4713H TYR* 4.4 19.5 - - + +
4776H TRP* 5.1 11.3 - - + -
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Residues in contact with LYS4673 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4231H SER* 5.3 8.5 - - - +
4669H PHE* 3.0 30.2 + - + +
4670H LYS* 4.5 4.3 - - - +
4672H GLU* 1.3 78.3 - - - +
4674H GLU* 1.3 57.7 + - - +
4676H ALA* 4.0 1.0 - - - +
4677H ARG* 3.0 29.5 + - - +
4713H TYR* 3.6 28.2 + - + -
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Residues in contact with GLU4674 (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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4670H LYS 3.8 12.6 + - - +
4671H ARG* 3.3 11.3 + - + +
4673H LYS* 1.3 78.5 - - - +
4675H LEU* 1.3 58.1 + - - +
4677H ARG* 3.7 4.8 + - - +
4678H LYS* 3.0 28.1 + - - +
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Residues in contact with LEU4675 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4671H ARG* 3.0 18.8 + - + +
4672H GLU* 3.8 8.1 - - - +
4674H GLU* 1.3 75.3 - - - +
4676H ALA* 1.3 63.2 + - - +
4678H LYS* 3.2 7.1 + - + +
4679H LEU* 3.2 32.6 + - + +
4684H LEU* 3.9 27.6 - - + -
4700H ASP* 4.6 15.7 - - + -
4703H VAL* 3.7 28.0 - - + -
4704H LEU* 4.7 6.3 - - + -
4709H PHE* 3.7 26.9 - - + -
4776H TRP* 4.9 8.7 - - + -
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Residues in contact with ALA4676 (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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4672H GLU 2.9 17.7 + - - +
4673H LYS 4.0 0.9 - - - +
4675H LEU* 1.3 78.3 - - - +
4677H ARG* 1.3 60.4 + - - +
4679H LEU* 3.4 14.2 + - - +
4680H GLU* 3.7 8.8 + - - +
4709H PHE* 6.0 3.6 - - + -
4713H TYR* 4.0 34.3 - - + +
4718H VAL* 3.9 30.0 - - + +
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Residues in contact with ARG4677 (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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4673H LYS 3.0 18.6 + - - +
4674H GLU* 4.1 4.9 - - - +
4676H ALA* 1.3 75.7 - - - +
4678H LYS* 1.3 62.0 + - - +
4679H LEU 3.3 0.2 - - - -
4680H GLU* 3.6 7.9 + - - +
4681H PHE* 3.4 20.1 + - - +
4713H TYR* 5.3 2.2 + - - +
5017H TRP* 6.4 2.5 - - + -
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Residues in contact with LYS4678 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4674H GLU 3.0 19.3 + - - +
4675H LEU* 3.2 12.3 + - + +
4677H ARG* 1.3 74.1 - - - +
4679H LEU* 1.3 64.1 + - + +
4680H GLU 3.4 0.2 - - - -
4681H PHE* 2.8 27.6 - - - +
4682H ASP 3.4 7.5 - - - +
4683H GLY* 3.3 14.7 - - - -
4684H LEU* 5.5 3.6 - - + +
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Residues in contact with LEU4679 (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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4675H LEU* 3.2 38.2 + - + +
4676H ALA 3.7 9.0 - - - +
4677H ARG 3.3 0.6 - - - -
4678H LYS* 1.3 78.3 - - + +
4680H GLU* 1.3 63.7 + - - +
4681H PHE 3.2 6.5 - - - +
4683H GLY* 4.8 6.0 + - - -
4684H LEU* 4.5 13.0 - - + -
4686H ILE* 5.9 0.9 - - - +
4704H LEU* 5.1 7.2 - - + -
4709H PHE* 4.1 21.3 - - + -
4718H VAL* 4.0 30.5 - - + +
4719H LYS* 4.8 6.3 - - + -
4722H VAL* 3.7 37.1 - - + +
4726H HIS* 4.9 2.3 - - - -
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Residues in contact with GLU4680 (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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4676H ALA 3.7 7.3 + - - +
4677H ARG* 3.6 10.2 + - - +
4678H LYS 3.4 0.4 - - - -
4679H LEU* 1.3 79.1 - - - +
4681H PHE* 1.3 60.4 + - - +
4721H LYS* 6.4 2.7 - - + -
4722H VAL* 5.7 2.9 - - - +
4725H LYS* 5.3 6.5 - - - +
4726H HIS* 4.3 11.8 + - - -
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Residues in contact with PHE4681 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4677H ARG 3.4 13.5 + - - +
4678H LYS* 2.8 14.7 - - - +
4679H LEU 3.2 10.2 - - - +
4680H GLU* 1.3 78.9 - - - +
4682H ASP* 1.3 66.1 + - - +
4683H GLY 3.0 2.6 + - - -
4726H HIS* 4.1 11.0 + - - -
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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