Contacts of the helix formed by residues 28 - 35 (chain C) in PDB entry 7CHW
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 LEU 28 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C TYR* 3.0 25.2 + - + +
27C LEU* 1.3 84.9 - - - +
29C SER* 1.3 60.2 + - - +
30C ILE* 3.2 4.9 - - - +
31C GLN* 3.6 5.6 + - + +
32C LEU* 3.1 33.5 + - + +
133C ASN* 3.7 26.2 - - + +
524C ILE* 3.6 21.1 - - + +
527C LYS* 3.3 45.1 - - + +
528C ARG* 4.8 2.9 - - + +
711C ASP 3.7 20.0 - - - +
712C SER* 5.0 3.4 - - - -
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO* 5.6 1.6 - - - +
26C TYR* 3.3 29.9 + - - +
27C LEU 3.8 0.4 - - - -
28C LEU* 1.3 76.1 - - - +
30C ILE* 1.3 66.2 + - - +
32C LEU* 4.6 1.3 - - - +
33C ASP* 3.0 46.2 + - - +
528C ARG* 5.3 1.0 - - - +
580C GLN* 6.0 4.0 - - - -
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.2 3.0 - - - -
29C SER* 1.3 80.4 - - - +
31C GLN* 1.3 64.4 + - + +
34C SER* 3.5 21.3 - - - -
147C SER* 3.5 25.6 - - - +
453C ILE* 5.6 0.9 - - + -
455C SER* 3.8 11.3 + - - +
527C LYS 4.1 16.4 - - - +
528C ARG* 5.2 13.2 - - + +
529C ARG 5.6 0.7 - - - +
530C ILE* 5.1 5.8 - - + -
575C LEU* 3.4 35.0 - - + -
579C ALA 6.0 0.4 - - - +
580C GLN* 5.7 2.2 - - - -
581C THR* 4.0 29.8 - - + +
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Residues in contact with GLN 31 (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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28C LEU* 3.6 8.3 + - + +
30C ILE* 1.3 76.3 - - + +
32C LEU* 1.3 64.4 + - + +
33C ASP 3.1 3.0 + - - -
34C SER* 3.2 11.2 + - - -
35C PHE* 3.4 9.5 + - - +
130C MET* 3.9 16.0 - - + +
134C GLY* 3.4 32.6 + - - +
136C PHE* 5.0 1.8 - - - -
144C VAL* 4.2 10.0 - - - +
145C ILE* 3.1 29.5 + - - +
146C VAL* 4.7 0.3 - - - -
147C SER* 4.1 11.6 + - - -
455C SER* 5.7 0.5 - - - -
456C VAL* 3.7 20.2 - - - +
527C LYS* 3.7 40.3 - - + +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 3.3 41.1 - - + +
28C LEU* 3.1 23.0 + - + +
29C SER* 4.9 1.3 - - - -
31C GLN* 1.3 78.6 - - - +
33C ASP* 1.3 65.0 + - - +
35C PHE* 4.4 0.8 - - - +
36C GLN* 3.8 18.0 + - - +
130C MET* 4.1 18.6 - - - -
131C THR 4.3 3.1 - - - +
132C ASP* 3.8 25.6 - - - +
133C ASN 4.9 0.4 - - - -
134C GLY* 4.1 10.8 - - - +
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Residues in contact with ASP 33 (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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29C SER* 3.0 36.7 + - - +
30C ILE 4.9 0.2 - - - +
31C GLN 3.1 0.6 - - - -
32C LEU* 1.3 83.8 - - - +
34C SER* 1.3 58.2 + - - +
35C PHE 3.3 1.5 + - - -
36C GLN* 3.6 5.0 + - - +
37C LYS* 3.2 37.2 + - - +
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Residues in contact with SER 34 (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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30C ILE 3.5 11.3 + - - -
31C GLN* 3.2 4.6 + - - -
33C ASP* 1.3 79.1 - - - +
35C PHE* 1.3 58.3 + - - +
37C LYS* 4.2 10.6 - - - +
38C PHE 4.3 4.0 + - - -
455C SER* 3.0 35.8 - - - -
456C VAL* 4.5 1.6 - - - -
457C GLY* 3.0 30.5 + - - -
458C GLU* 4.5 2.6 + - - +
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Residues in contact with PHE 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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31C GLN 3.4 4.9 + - - +
32C LEU 5.1 0.7 - - - +
33C ASP 3.3 0.2 - - - -
34C SER* 1.3 78.3 - - - +
36C GLN* 1.3 62.4 + - - +
37C LYS 3.1 1.3 - - - -
38C PHE* 3.3 30.6 + + + +
39C ILE* 3.3 45.6 + - + +
127C ILE* 4.7 0.4 - - + -
128C PRO 3.4 24.2 - - - -
129C LEU* 4.4 3.1 - - + -
130C MET* 3.4 56.5 - - + -
136C PHE* 4.0 19.3 - + - -
456C VAL* 4.5 11.4 - - + -
457C GLY* 5.2 1.8 - - - -
460C ALA* 5.2 1.1 - - + -
506C PHE* 4.6 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
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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