Contacts of the helix formed by residues 26 - 35 (chain C) in PDB entry 6C9G
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 SER 26 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN* 1.3 78.8 - - - +
27C VAL* 1.3 74.0 + - - +
28C TYR* 3.3 12.0 + - - +
29C THR* 3.4 25.0 - - - -
30C SER* 3.1 20.8 + - - -
187C PHE* 5.2 7.4 - - - -
321C LEU* 4.6 3.7 + - - -
323C LEU 4.7 2.5 - - - -
324C THR 3.5 30.4 + - - -
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Residues in contact with VAL 27 (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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26C SER* 1.3 77.0 + - - +
28C TYR* 1.3 74.0 + - + +
30C SER* 2.6 25.7 + - - -
31C PHE* 3.8 4.2 + - - +
178C PHE* 4.7 4.4 - - + -
182C PHE* 3.3 62.6 - - + -
185C PRO* 5.0 7.0 - - + -
187C PHE* 6.2 3.6 - - + -
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Residues in contact with TYR 28 (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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26C SER* 3.3 6.8 + - - +
27C VAL* 1.3 89.1 - - + +
29C THR* 1.3 63.4 + - - +
31C PHE* 3.4 10.6 + - + +
32C MET* 3.3 27.1 + - + +
175C LEU* 4.8 10.0 - - + +
178C PHE* 4.5 11.4 - + - -
179C ILE* 3.2 57.1 + - + +
182C PHE* 4.8 5.8 - + + -
185C PRO* 3.3 39.4 - - + +
187C PHE* 5.6 6.5 - + + -
188C MET* 4.2 13.4 - - - -
321C LEU* 4.1 43.5 - - + +
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Residues in contact with THR 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASN* 4.3 8.5 - - + +
26C SER* 3.3 30.7 + - - +
27C VAL 3.3 0.4 - - - -
28C TYR* 1.3 77.4 - - - +
30C SER* 1.3 65.8 + - - +
32C MET* 3.2 10.0 + - - +
33C LYS* 3.1 36.9 + - - +
138C PHE* 3.4 24.7 - - + -
321C LEU 3.2 17.7 + - - -
322C VAL 3.2 12.7 + - - +
323C LEU 4.6 0.9 + - - -
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Residues in contact with SER 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASN* 4.5 17.5 - - - +
26C SER 3.1 11.2 + - - -
27C VAL* 2.6 25.6 + - - -
29C THR* 1.3 77.1 - - - +
31C PHE* 1.3 59.0 + - - +
33C LYS* 3.2 6.7 + - - +
34C SER* 2.8 32.6 + - - -
178C PHE* 5.7 1.2 - - - -
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Residues in contact with PHE 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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334A ARG* 5.5 2.9 - - - -
27C VAL 4.4 0.9 - - - +
28C TYR 3.4 10.7 + - - +
29C THR 3.2 0.4 - - - -
30C SER* 1.3 82.4 + - - +
32C MET* 1.3 62.1 + - - +
34C SER* 3.2 8.9 + - - -
35C HIS* 2.9 56.5 + + - +
137C LEU* 5.2 0.7 - - + -
174C PHE* 3.2 37.2 - + - -
175C LEU* 3.4 36.3 - - + -
178C PHE* 3.2 69.1 - + + -
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Residues in contact with MET 32 (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 TYR 3.3 16.1 + - - +
29C THR* 3.2 9.9 + - - +
31C PHE* 1.3 80.5 - - + +
33C LYS* 1.3 58.4 + - - +
34C SER 3.6 0.2 + - - -
35C HIS 3.7 2.1 - - - +
136C SER* 3.5 0.2 - - - -
137C LEU* 3.0 24.1 + - + +
138C PHE* 2.7 40.6 + - + +
141C VAL* 3.8 30.5 - - - -
171C ILE* 5.1 1.8 - - - -
175C LEU* 4.0 37.2 - - + -
318C LEU* 5.1 3.8 - - + +
321C LEU* 3.5 30.1 - - + +
322C VAL* 3.7 17.0 - - + +
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Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASN* 3.9 25.9 + - - +
29C THR* 3.1 31.7 + - + +
30C SER* 3.2 7.8 + - - +
32C MET* 1.3 75.9 - - - +
34C SER* 1.3 65.2 + - - +
136C SER* 3.2 22.3 - - - +
138C PHE* 3.6 34.6 - - + -
139C ASP* 5.8 0.2 - - - +
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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 SER* 2.8 20.7 + - - -
31C PHE* 3.2 4.1 + - - -
33C LYS* 1.3 81.5 - - - +
35C HIS* 1.3 81.5 + - - +
36C ARG* 3.7 6.2 + - - +
136C SER* 5.1 0.2 - - - -
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Residues in contact with HIS 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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331A ASP* 5.2 5.4 + - - -
334A ARG* 6.3 0.8 - - - -
335A ILE* 4.8 11.0 - - + +
31C PHE* 2.9 50.5 + + - +
33C LYS 3.5 0.2 - - - -
34C SER* 1.3 87.3 - - - +
36C ARG* 1.3 65.3 + - - +
39C ASP* 3.2 22.2 - - - +
136C SER* 3.2 4.1 - - - -
137C LEU* 2.8 43.2 + - + +
174C PHE* 3.8 21.2 - + + -
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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