Contacts of the helix formed by residues 34 - 43 (chain C) in PDB entry 6DDE
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 ALA 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.7 14.8 - - + -
33B ILE* 4.6 8.1 - - + +
261B LEU* 3.7 28.5 - - + -
30C VAL* 2.5 25.7 + - + +
31C SER* 5.4 0.2 - - - -
33C ALA* 1.3 74.6 - - - +
35C ALA* 1.3 58.0 + - - +
36C ASP 3.1 1.1 - - - -
37C LEU* 3.1 29.3 + - + +
38C MET* 3.3 7.4 + - - +
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.3 19.3 - - + +
30C VAL 4.0 2.6 + - - -
31C SER 3.5 19.4 + - - +
32C LYS* 5.2 2.5 - - - -
33C ALA 4.3 0.4 - - - +
34C ALA* 1.3 77.2 - - - +
36C ASP* 1.3 60.0 + - - +
38C MET* 3.9 5.6 - - - +
39C ALA* 2.9 30.1 + - - +
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASN* 6.4 0.2 - - - +
256B ARG* 5.1 8.8 + - - -
32C LYS 3.6 19.2 - - - +
33C ALA* 4.3 12.1 - - - +
34C ALA* 3.1 1.2 - - - +
35C ALA* 1.3 78.6 - - - +
37C LEU* 1.3 60.9 + - + +
39C ALA* 4.0 5.8 - - - +
40C TYR* 2.9 31.5 + - - +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B PHE* 3.6 44.2 - - + -
237B ASN* 5.0 6.5 - - + -
239B ASN* 5.0 10.1 - - + +
240B ALA* 4.5 12.1 - - + -
252B LEU* 5.5 4.9 - - + -
254B ASP* 4.2 15.9 - - - +
261B LEU* 5.7 4.3 - - + -
300B LEU* 3.8 20.9 - - + +
33C ALA 3.6 22.2 - - - +
34C ALA* 3.1 16.1 + - + +
36C ASP* 1.3 82.1 - - + +
38C MET* 1.3 56.9 + - - +
40C TYR* 3.6 3.9 - - - +
41C CYS* 2.9 31.9 + - - +
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Residues in contact with MET 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.4 23.1 - - + +
36B ASN* 5.5 4.5 - - + -
37B ILE* 3.7 46.4 - - + +
300B LEU* 3.9 13.6 - - + +
34C ALA 3.3 9.2 + - - +
35C ALA* 3.5 9.2 + - - +
37C LEU* 1.3 78.9 - - - +
39C ALA* 1.3 62.0 + - - +
41C CYS* 4.2 0.3 - - - +
42C GLU* 2.9 43.6 + - + +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ALA 2.9 20.1 + - - +
36C ASP* 4.0 6.5 - - - +
38C MET* 1.3 80.1 - - - +
40C TYR* 1.3 60.4 + - - +
42C GLU* 3.6 6.6 + - - +
43C ALA* 3.0 29.3 + - - +
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Residues in contact with TYR 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B PHE* 3.7 31.4 - + - -
236B PRO* 3.5 26.4 + - + +
237B ASN* 4.0 25.4 - - + -
280B LYS 4.1 6.8 + - - -
281B SER* 3.8 13.7 - - - -
36C ASP 2.9 19.7 + - - +
37C LEU* 3.6 3.8 - - - +
39C ALA* 1.3 75.9 - - - +
41C CYS* 1.3 62.4 + - + +
43C ALA* 2.9 21.9 + - - +
44C HIS* 3.0 48.4 + + + -
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Residues in contact with CYS 41 (chain C).
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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37B ILE* 6.1 0.2 - - + -
235B PHE* 4.9 2.7 - - + -
281B SER* 3.3 26.9 - - - +
282B GLY 3.9 1.8 - - - -
283B ARG* 3.5 47.5 + - - +
300B LEU* 3.7 14.4 - - + -
37C LEU 2.9 19.0 + - - +
38C MET 4.2 0.7 - - - +
40C TYR* 1.3 82.6 - - + +
42C GLU* 1.3 57.4 + - - +
44C HIS* 3.8 2.4 - - - +
45C ALA* 3.2 25.8 + - - +
51C LEU* 5.6 0.7 - - - -
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ILE* 5.2 8.8 - - + +
283B ARG* 5.9 1.1 - - - +
38C MET* 2.9 35.3 + - + +
39C ALA* 3.9 6.4 - - - +
41C CYS* 1.3 76.9 - - - +
43C ALA* 1.3 62.9 + - - +
44C HIS 3.2 3.1 + - - -
45C ALA* 3.7 15.5 + - + +
46C LYS* 5.0 8.0 + - - +
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA 3.0 18.1 + - - +
40C TYR* 2.9 10.7 + - - +
42C GLU* 1.3 78.7 + - - +
44C HIS* 1.3 73.3 + - + +
45C ALA 3.8 0.2 - - - -
46C LYS* 4.5 10.1 + - - +
47C GLU* 4.1 6.6 - - - +
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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