Contacts of the helix formed by residues 173 - 178 (chain C) in PDB entry 3K9S
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 TYR 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ASP* 5.5 1.6 - - - -
22C THR* 5.4 1.6 - - - -
168C VAL 3.4 22.2 - - - -
169C TRP 3.5 12.8 - - - -
170C GLU* 3.1 29.7 + - + +
172C ALA* 1.3 79.8 - - - +
174C TYR* 1.3 61.4 + + - +
175C LEU 3.4 2.0 - - - -
176C LYS 4.2 1.3 - - - -
177C PHE* 2.8 47.1 + - + +
178C GLN 3.1 24.5 - - - -
179C ASN* 4.6 3.2 + - - -
181C ARG* 3.1 49.8 + - + +
184C TYR* 3.4 44.0 - + + -
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Residues in contact with TYR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLU* 2.9 31.0 + - + +
171C HIS 4.4 2.0 + - - -
173C TYR* 1.3 77.5 - + - +
175C LEU* 1.3 63.1 + - - +
178C GLN* 2.8 69.8 + - + +
179C ASN* 3.5 2.2 - - - -
22D THR* 6.0 0.6 - - + +
25D ILE* 3.4 17.5 - - - +
26D HIS 5.1 0.5 + - - -
30D HIS* 2.7 29.2 + + - -
171D HIS* 3.5 39.9 + - + +
174D TYR* 4.4 22.9 - - + -
175D LEU* 3.6 32.2 - - + +
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASP* 4.0 5.4 - - - +
21C GLN* 3.8 35.9 - - + +
22C THR* 3.3 25.7 + - - +
25C ILE* 3.9 20.2 - - + -
171C HIS 5.4 0.2 + - - -
173C TYR 3.4 0.6 - - - -
174C TYR* 1.3 76.7 - - - +
176C LYS* 1.3 56.8 + - - +
178C GLN* 2.9 14.6 + - - -
174D TYR* 3.8 39.7 - - + +
175D LEU* 4.3 17.6 - - + +
178D GLN* 4.1 11.0 - - + +
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Residues in contact with LYS 176 (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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15C GLU* 5.1 1.8 + - - -
16C PRO 2.8 29.3 + - - -
17C HIS* 3.0 15.9 + - - +
19C ASP* 3.5 35.9 + - + +
173C TYR 3.6 2.0 + - - -
175C LEU* 1.3 81.1 - - - +
177C PHE* 1.3 92.7 + - + +
178C GLN* 3.6 5.0 + - - -
180C ARG* 3.3 13.5 + - - -
187C GLU* 5.1 4.6 + - - -
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Residues in contact with PHE 177 (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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17C HIS 3.7 14.4 - - - -
18C PHE* 5.2 2.0 - + - -
19C ASP* 4.9 3.4 - - - -
172C ALA 5.6 0.4 - - - -
173C TYR* 2.8 37.2 + - + +
176C LYS* 1.3 113.4 - - + +
178C GLN* 1.3 67.7 + - - +
179C ASN 3.1 0.3 + - - -
180C ARG* 2.8 53.7 + - + +
183C ASP* 3.8 13.9 - - + -
184C TYR* 3.7 44.6 - + + -
187C GLU* 3.8 20.0 - - + -
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Residues in contact with GLN 178 (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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173C TYR* 3.1 19.5 + - - -
174C TYR* 2.8 63.3 + - + +
175C LEU 2.9 29.3 + - - -
176C LYS* 3.6 6.1 + - - +
177C PHE* 1.3 75.5 - - - +
179C ASN* 1.3 65.4 + - - +
180C ARG* 3.0 34.7 + - - +
21D GLN* 5.2 5.9 + - - -
25D ILE* 4.1 26.1 - - + +
175D LEU* 4.3 8.7 - - + +
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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