Contacts of the helix formed by residues 4221 - 4239 (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 GLY4221 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4219D GLU* 3.3 9.8 - - - +
4220D GLY* 1.3 76.5 - - - +
4222D GLU* 1.3 59.2 + - - -
4223D SER 3.4 2.7 - - - -
4224D GLU* 3.9 14.3 - - - +
4225D LYS* 3.1 27.9 + - - +
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Residues in contact with GLU4222 (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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4220D GLY 3.5 5.5 + - - +
4221D GLY* 1.3 70.1 - - - +
4223D SER* 1.3 65.7 + - - +
4225D LYS* 3.4 14.5 + - - +
4226D MET* 3.6 17.5 + - - +
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Residues in contact with SER4223 (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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4222D GLU* 1.3 76.4 - - - +
4224D GLU* 1.3 66.3 + - - +
4226D MET* 3.3 23.3 + - - +
4227D GLU* 4.0 3.3 + - - +
4971F HIS* 6.5 0.7 - - - -
4973F PHE* 5.1 17.5 - - - -
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Residues in contact with GLU4224 (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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4221D GLY* 3.7 15.7 + - - +
4222D GLU 3.3 0.4 - - - -
4223D SER* 1.3 78.3 - - - +
4225D LYS* 1.3 61.7 + - - +
4226D MET 3.4 0.7 + - - -
4227D GLU* 3.4 15.7 + - - +
4228D LEU* 3.6 12.6 + - - +
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Residues in contact with LYS4225 (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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4212D PHE* 5.3 1.2 - - - -
4216D VAL* 4.4 24.6 - - + +
4219D GLU* 4.8 7.4 - - + +
4221D GLY 3.1 19.9 + - - +
4222D GLU* 3.6 8.7 - - - +
4223D SER 3.2 0.6 - - - -
4224D GLU* 1.3 74.2 - - - +
4226D MET* 1.3 66.8 + - + +
4227D GLU 3.3 0.2 - - - -
4228D LEU* 3.3 23.8 + - + +
4229D PHE* 3.6 7.3 + - - +
4957D PHE* 5.0 14.1 - - + -
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Residues in contact with MET4226 (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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4222D GLU 3.6 16.4 - - - +
4223D SER* 3.5 13.0 - - - +
4224D GLU 3.2 0.8 - - - -
4225D LYS* 1.3 79.5 - - - +
4227D GLU* 1.3 60.9 + - - +
4229D PHE* 3.4 19.9 + - + +
4230D VAL* 3.9 9.0 - - - +
4957D PHE* 3.8 34.3 - - + +
4958D ILE* 5.3 4.3 - - - +
5017D TRP* 5.2 8.9 - - + +
5020D PHE* 3.7 48.2 - - + -
5022D ALA* 5.5 9.0 - - + -
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Residues in contact with GLU4227 (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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4223D SER 4.0 3.4 + - - +
4224D GLU* 3.4 12.4 + - - +
4225D LYS 3.3 0.4 - - - -
4226D MET* 1.3 76.5 - - - +
4228D LEU* 1.3 63.7 + - - +
4230D VAL* 3.4 19.4 + - - +
4231D SER* 3.6 10.6 + - - -
5017D TRP* 5.1 21.7 - - + +
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Residues in contact with LEU4228 (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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4212D PHE* 3.7 22.3 - - + -
4215D ASP 5.5 6.7 - - - +
4216D VAL* 5.7 7.4 - - + -
4224D GLU 3.6 9.2 + - - +
4225D LYS* 3.3 17.4 + - + +
4226D MET 3.2 0.6 - - - -
4227D GLU* 1.3 77.2 - - - +
4229D PHE* 1.3 64.5 + - - +
4231D SER* 3.5 11.7 + - - +
4232D PHE* 3.2 15.9 + - - +
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Residues in contact with PHE4229 (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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4212D PHE* 3.5 32.2 - + + -
4225D LYS 3.6 6.2 + - - +
4226D MET* 3.4 13.4 + - + +
4227D GLU 3.2 0.8 - - - -
4228D LEU* 1.3 76.8 - - - +
4230D VAL* 1.3 63.6 + - - +
4232D PHE* 3.2 15.4 + + - +
4233D CYS* 3.2 45.2 + - - -
4957D PHE* 4.6 14.6 - + + -
4958D ILE* 5.2 11.7 - - + -
4983D LEU 5.2 7.9 - - - -
4984D ALA* 6.5 0.2 - - - -
4986D TYR* 4.4 26.5 - + + -
4987D MET 5.8 0.4 - - - -
4990D LEU* 6.2 1.6 - - + -
5020D PHE* 3.5 35.0 - + + -
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Residues in contact with VAL4230 (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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4226D MET 3.9 14.4 - - - +
4227D GLU* 3.4 8.5 + - - +
4228D LEU 3.3 0.2 - - - -
4229D PHE* 1.3 77.5 - - - +
4231D SER* 1.3 61.2 + - - +
4233D CYS* 3.5 8.2 + - - +
4234D GLU* 3.4 20.3 + - - +
4990D LEU* 4.5 10.2 - - + +
5012D TYR* 3.6 34.0 + - + +
5017D TRP* 3.5 34.1 - - + +
5019D PHE* 4.1 16.4 - - + -
5020D PHE* 4.4 5.8 - - + -
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Residues in contact with SER4231 (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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4227D GLU 3.6 7.8 + - - -
4228D LEU* 3.5 18.9 + - - -
4229D PHE 3.3 0.4 - - - -
4230D VAL* 1.3 76.1 - - - +
4232D PHE* 1.3 63.0 - - - +
4234D GLU* 3.7 8.2 + - - +
4235D ASP* 3.5 19.6 + - - +
4669D PHE* 5.6 0.7 - - - -
4673D LYS* 5.3 8.1 - - - +
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Residues in contact with PHE4232 (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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4200D TRP* 5.9 8.3 - + - -
4205D VAL 5.2 1.6 - - - -
4208D SER* 3.2 43.7 - - - -
4209D LYS* 3.7 19.3 - - + -
4212D PHE* 3.6 50.0 - + + -
4228D LEU 3.2 3.8 + - - -
4229D PHE* 3.2 16.5 + + - +
4230D VAL 3.2 1.0 - - - -
4231D SER* 1.3 75.8 - - - +
4233D CYS* 1.3 73.2 + - - +
4235D ASP* 3.3 13.8 + - + +
4236D THR* 3.3 30.4 + - + +
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Residues in contact with CYS4233 (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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4229D PHE* 3.2 46.4 + - - -
4230D VAL* 3.5 6.7 + - - +
4231D SER 3.4 0.2 - - - -
4232D PHE* 1.3 82.0 - - - +
4234D GLU* 1.3 61.6 + - - +
4236D THR* 2.7 27.0 + - - -
4237D ILE* 3.2 13.9 - - + +
4986D TYR 5.3 0.2 - - - -
4987D MET* 4.3 25.6 - - + -
4990D LEU* 4.5 22.4 - - + -
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Residues in contact with GLU4234 (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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4230D VAL 3.4 14.4 + - - +
4231D SER* 4.0 9.0 - - - +
4232D PHE 3.3 0.6 - - - -
4233D CYS* 1.3 78.7 - - - +
4235D ASP* 1.3 61.1 + - - +
4238D PHE 3.5 8.0 + - - -
4669D PHE* 3.5 23.1 - - + -
4714D TRP* 3.5 41.4 - - + -
4990D LEU* 5.7 1.7 - - + +
5012D TYR* 5.3 4.5 - - - +
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Residues in contact with ASP4235 (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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4231D SER 3.5 10.5 + - - +
4232D PHE* 3.3 11.8 + - + +
4233D CYS 3.2 0.6 - - - -
4234D GLU* 1.3 76.5 - - - +
4236D THR* 1.3 65.0 + - + +
4238D PHE* 3.5 8.8 + - - +
4239D GLU* 3.3 20.0 + - - +
4666D LEU* 3.9 26.4 - - + +
4669D PHE* 4.1 13.7 - - + -
4670D LYS* 6.5 0.4 - - + -
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Residues in contact with THR4236 (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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4200D TRP* 6.1 5.6 - - + -
4205D VAL* 4.8 15.6 - - + +
4208D SER* 5.5 2.5 - - - +
4232D PHE* 3.3 39.3 - - + +
4233D CYS* 2.7 22.4 + - - -
4235D ASP* 1.3 76.6 - - + +
4237D ILE* 1.3 68.8 + - - +
4239D GLU* 3.0 42.3 + - - +
4987D MET* 4.4 7.9 - - + +
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Residues in contact with ILE4237 (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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4196D ASN* 4.8 4.0 - - - +
4233D CYS* 3.2 15.2 + - + +
4234D GLU 3.7 0.2 + - - -
4235D ASP 3.4 0.2 - - - -
4236D THR* 1.3 87.1 - - - +
4238D PHE* 1.3 61.2 + - - +
4239D GLU 3.4 6.3 + - - +
4714D TRP* 3.6 31.2 - - + -
4987D MET* 4.5 20.6 - - + +
4990D LEU* 6.2 2.5 - - + -
4991D MET* 3.7 39.5 - - + +
4994D ILE* 5.9 6.3 - - + -
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Residues in contact with PHE4238 (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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4234D GLU 3.5 11.1 + - - +
4235D ASP 3.5 10.0 + - - +
4236D THR 3.2 0.8 - - - -
4237D ILE* 1.3 79.4 - - - +
4239D GLU* 1.3 62.4 + - + +
4665D PRO* 3.2 42.6 - - + -
4666D LEU* 4.9 6.3 - - + -
4669D PHE* 4.1 21.3 - + + -
4711D SER 5.3 0.2 - - - -
4712D ASN* 3.2 56.8 - - + -
4714D TRP* 4.7 10.5 - + - +
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Residues in contact with GLU4239 (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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4204D GLN* 4.3 14.8 - - - +
4205D VAL* 3.3 31.2 - - - +
4235D ASP 3.3 15.7 - - - +
4236D THR* 3.0 28.3 - - - +
4237D ILE* 3.2 8.3 - - - +
4238D PHE* 1.3 82.6 - - + +
4662D LEU 5.7 4.9 - - - +
4666D 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
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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