Contacts of the helix formed by residues 4221 - 4239 (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 GLY4221 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4219H GLU* 3.3 9.1 - - - +
4220H GLY* 1.3 75.7 - - - +
4222H GLU* 1.3 59.9 + - - -
4223H SER 3.4 2.7 - - - -
4224H GLU* 3.9 14.8 - - - +
4225H LYS* 3.1 27.7 + - - +
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Residues in contact with GLU4222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4220H GLY 3.5 5.6 + - - +
4221H GLY* 1.3 69.7 - - - -
4223H SER* 1.3 64.9 + - - +
4225H LYS* 3.4 13.8 + - - +
4226H MET* 3.6 17.3 + - - +
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Residues in contact with SER4223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4971B HIS* 6.5 1.1 - - - -
4973B PHE* 5.1 17.0 - - - -
4221H GLY* 4.5 0.4 - - - -
4222H GLU* 1.3 76.7 - - - +
4224H GLU* 1.3 65.1 + - - +
4226H MET* 3.3 23.1 + - - +
4227H GLU* 4.0 3.8 + - - +
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Residues in contact with GLU4224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4221H GLY* 3.7 15.9 + - - +
4222H GLU 3.3 0.4 - - - -
4223H SER* 1.3 80.0 - - - +
4225H LYS* 1.3 62.1 + - - +
4226H MET 3.4 0.3 + - - -
4227H GLU* 3.4 15.3 + - - +
4228H LEU* 3.6 13.0 + - - +
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Residues in contact with LYS4225 (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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4212H PHE* 5.3 1.2 - - - -
4216H VAL* 4.4 25.0 - - + +
4219H GLU* 4.8 7.2 - - + -
4221H GLY 3.1 19.6 + - - +
4222H GLU* 3.6 9.2 - - - +
4223H SER 3.2 0.6 - - - -
4224H GLU* 1.3 74.7 - - - +
4226H MET* 1.3 64.5 + - - +
4227H GLU 3.3 0.2 - - - -
4228H LEU* 3.3 24.5 + - + +
4229H PHE* 3.6 7.3 + - - +
4957H PHE* 5.0 15.0 - - + -
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Residues in contact with MET4226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4222H GLU 3.6 15.7 - - - +
4223H SER* 3.5 13.2 - - - +
4224H GLU 3.2 1.2 - - - -
4225H LYS* 1.3 79.5 - - - +
4227H GLU* 1.3 60.8 + - - +
4229H PHE* 3.4 19.5 + - + +
4230H VAL* 3.9 9.4 - - - +
4957H PHE* 3.8 34.1 - - + +
4958H ILE* 5.3 3.8 - - - +
5017H TRP* 5.2 8.5 - - + +
5020H PHE* 3.7 48.5 - - + -
5022H ALA* 5.5 8.7 - - + -
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Residues in contact with GLU4227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4223H SER 4.0 3.6 + - - +
4224H GLU* 3.4 11.1 + - - +
4225H LYS 3.3 0.6 - - - -
4226H MET* 1.3 76.7 - - - +
4228H LEU* 1.3 64.1 + - - +
4230H VAL* 3.4 19.3 + - - +
4231H SER* 3.6 9.7 + - - -
5017H TRP* 5.1 21.5 - - + +
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Residues in contact with LEU4228 (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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4212H PHE* 3.7 20.9 - - + -
4215H ASP 5.5 6.3 - - - +
4216H VAL* 5.7 7.0 - - + -
4224H GLU 3.6 9.8 + - - +
4225H LYS* 3.3 19.2 + - + +
4226H MET 3.2 1.0 - - - -
4227H GLU* 1.3 76.1 - - - +
4229H PHE* 1.3 64.2 + - - +
4230H VAL 3.3 0.2 - - - -
4231H SER* 3.5 12.6 + - - +
4232H PHE* 3.2 15.4 + - - +
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Residues in contact with PHE4229 (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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4212H PHE* 3.5 33.6 - + + -
4225H LYS 3.6 6.4 + - - +
4226H MET* 3.4 14.4 + - + +
4227H GLU 3.2 0.6 - - - -
4228H LEU* 1.3 77.4 - - - +
4230H VAL* 1.3 64.5 + - - +
4232H PHE* 3.2 16.5 + + - +
4233H CYS* 3.2 44.4 + - - -
4957H PHE* 4.6 14.4 - + + -
4958H ILE* 5.2 11.9 - - + -
4983H LEU 5.2 8.3 - - - -
4984H ALA* 6.5 0.2 - - - -
4986H TYR* 4.4 25.6 - + + -
4987H MET 5.8 0.2 - - - -
4990H LEU* 6.2 2.0 - - + -
5020H PHE* 3.5 34.3 - + + -
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Residues in contact with VAL4230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4226H MET 3.9 14.8 - - - +
4227H GLU* 3.4 8.5 + - - +
4228H LEU 3.3 0.4 - - - -
4229H PHE* 1.3 77.7 - - - +
4231H SER* 1.3 61.6 + - - +
4232H PHE 3.4 0.2 + - - -
4233H CYS* 3.5 7.7 + - - +
4234H GLU* 3.4 20.8 + - - +
4990H LEU* 4.5 10.1 - - + +
5012H TYR* 3.6 34.5 + - + +
5017H TRP* 3.5 34.1 - - + +
5019H PHE* 4.1 16.4 - - + -
5020H PHE* 4.4 6.1 - - + -
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Residues in contact with SER4231 (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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4227H GLU 3.6 8.5 + - - -
4228H LEU* 3.5 18.5 + - - -
4229H PHE 3.3 0.6 - - - -
4230H VAL* 1.3 77.3 - - - +
4232H PHE* 1.3 61.8 + - - +
4234H GLU* 3.7 7.5 + - - +
4235H ASP* 3.5 20.6 + - - +
4669H PHE* 5.6 0.7 - - - -
4673H LYS* 5.3 8.8 - - - +
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Residues in contact with PHE4232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4200H TRP* 5.9 7.9 - + - -
4205H VAL 5.2 2.0 - - - -
4208H SER* 3.2 40.6 - - - -
4209H LYS* 3.7 21.1 - - + -
4212H PHE* 3.6 50.0 - + + -
4228H LEU 3.2 4.2 + - - +
4229H PHE* 3.2 15.8 + + - +
4230H VAL 3.2 0.6 - - - -
4231H SER* 1.3 75.8 - - - +
4233H CYS* 1.3 74.6 + - - +
4235H ASP* 3.3 13.8 + - + +
4236H THR* 3.3 31.9 + - + +
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Residues in contact with CYS4233 (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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4229H PHE* 3.2 45.9 + - - -
4230H VAL* 3.5 6.9 + - - +
4231H SER 3.4 0.2 - - - -
4232H PHE* 1.3 79.3 - - - +
4234H GLU* 1.3 64.6 + - - +
4236H THR* 2.7 27.0 + - - -
4237H ILE* 3.2 14.9 - - + +
4986H TYR 5.3 0.2 - - - -
4987H MET* 4.3 26.0 - - + -
4990H LEU* 4.5 22.2 - - + -
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Residues in contact with GLU4234 (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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4230H VAL 3.4 14.6 + - - +
4231H SER* 4.0 8.7 - - - +
4232H PHE 3.3 0.6 - - - -
4233H CYS* 1.3 79.1 - - - +
4235H ASP* 1.3 60.9 + - - +
4238H PHE 3.5 8.1 + - - -
4669H PHE* 3.5 23.3 - - + -
4714H TRP* 3.5 41.7 - - + -
4990H LEU* 5.7 1.9 - - + +
5012H TYR* 5.3 5.2 - - - +
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Residues in contact with ASP4235 (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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4231H SER 3.5 10.4 + - - +
4232H PHE* 3.3 13.3 + - + +
4233H CYS 3.2 0.6 - - - -
4234H GLU* 1.3 77.4 - - - +
4236H THR* 1.3 64.7 + - + +
4238H PHE* 3.5 8.8 + - - +
4239H GLU* 3.3 19.1 + - - +
4666H LEU* 3.9 26.2 - - + +
4669H PHE* 4.1 13.6 - - + -
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Residues in contact with THR4236 (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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4200H TRP* 6.1 5.4 - - + -
4205H VAL* 4.8 15.8 - - + +
4208H SER* 5.5 2.7 - - - +
4232H PHE* 3.3 38.4 - - + +
4233H CYS* 2.7 21.4 + - - -
4235H ASP* 1.3 77.9 - - + +
4237H ILE* 1.3 69.4 + - - +
4239H GLU* 3.0 43.5 + - - +
4987H MET* 4.4 8.8 - - + +
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Residues in contact with ILE4237 (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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4196H ASN* 4.8 4.5 - - - +
4233H CYS* 3.2 15.9 + - + +
4234H GLU 3.7 0.4 + - - -
4235H ASP 3.4 0.2 - - - -
4236H THR* 1.3 88.3 - - - +
4238H PHE* 1.3 63.7 + - - +
4239H GLU 3.4 5.9 + - - +
4714H TRP* 3.6 31.2 - - + +
4987H MET* 4.5 20.6 - - + +
4990H LEU* 6.2 3.6 - - + -
4991H MET* 3.7 38.1 - - + +
4994H ILE* 5.9 6.3 - - + -
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Residues in contact with PHE4238 (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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4234H GLU 3.5 11.3 + - - +
4235H ASP 3.5 10.0 + - - +
4236H THR 3.2 0.8 - - - -
4237H ILE* 1.3 78.6 - - - +
4239H GLU* 1.3 63.1 + - + +
4665H PRO* 3.2 41.5 - - + -
4666H LEU* 4.9 5.8 - - + -
4669H PHE* 4.1 21.5 - + + -
4711H SER 5.3 0.4 - - - -
4712H ASN* 3.2 56.5 - - + -
4714H TRP* 4.7 10.5 - + - +
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Residues in contact with GLU4239 (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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4204H GLN* 4.3 15.1 - - - +
4205H VAL* 3.3 30.9 - - - +
4235H ASP 3.3 15.0 - - - +
4236H THR* 3.0 27.7 - - - +
4237H ILE 3.5 7.8 - - - +
4238H PHE* 1.3 84.3 - - + +
4662H LEU 5.7 4.7 - - - +
4666H LEU* 5.6 12.8 - - + -
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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