Contacts of the helix formed by residues 180 - 185 (chain P) in PDB entry 5C7O
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 180 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176P ILE* 2.9 20.0 + - - -
177P GLN* 2.7 23.7 + - - +
179P ALA* 1.3 76.1 - - - +
181P ASP* 1.3 60.6 + - - +
182P HIS 3.0 0.2 - - - -
183P ILE* 2.9 26.1 + - - +
184P SER* 3.2 10.0 + - - -
217P ASN* 5.4 2.0 - - - -
218P ILE* 3.4 19.7 - - - +
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Residues in contact with ASP 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153P PRO* 4.0 6.1 - - + +
154P LYS* 3.8 38.5 + - - +
177P GLN 4.1 8.5 - - - +
178P ALA* 3.5 14.9 + - - +
179P ALA 3.1 0.2 - - - -
180P SER* 1.3 80.9 + - - +
182P HIS* 1.3 60.6 + - - +
184P SER* 2.8 25.4 + - - -
185P ALA* 3.1 12.3 + - - +
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Residues in contact with HIS 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P ASN* 3.5 24.9 - - + -
153P PRO* 3.5 27.2 - - + +
156P ILE* 3.7 11.0 - - + -
158P TRP* 3.0 24.1 + - - +
166P VAL* 3.9 10.7 - - + +
168P GLU* 2.8 26.1 + - + +
179P ALA* 2.9 29.2 + - - +
181P ASP* 1.3 78.8 - - - +
183P ILE* 1.3 59.8 + - - +
185P ALA* 3.1 10.4 + - - +
186P GLY 3.1 1.0 + - - -
187P ALA* 2.9 30.1 + - + +
190P VAL* 3.6 26.2 - - + -
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Residues in contact with ILE 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P ARG* 4.6 2.3 + - - -
180P SER* 2.9 22.4 + - - +
182P HIS* 1.3 76.1 - - - +
184P SER* 1.3 57.7 + - - +
186P GLY* 2.9 20.4 + - - -
187P ALA 3.5 23.7 + - - +
188P GLN 3.9 19.1 - - - +
189P ARG* 4.0 4.0 - - - -
190P VAL* 4.0 19.5 - - + -
217P ASN* 3.7 33.0 - - + +
218P ILE* 4.4 3.1 - - + -
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Residues in contact with SER 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P LYS* 4.7 6.4 + - - +
159P ARG* 2.8 29.8 + - - +
180P SER 3.2 7.3 + - - -
181P ASP* 2.8 27.4 + - - +
183P ILE* 1.3 79.7 - - - +
185P ALA* 1.3 53.4 + - - +
186P GLY 3.2 0.4 - - - -
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Residues in contact with ALA 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153P PRO 3.5 14.6 - - - +
154P LYS 3.5 14.1 - - - +
156P ILE 3.3 19.7 - - - +
157P PRO* 4.4 0.7 - - - +
158P TRP* 3.5 23.9 + - + +
159P ARG* 3.5 17.3 + - - +
181P ASP 3.1 14.0 + - - +
182P HIS 3.5 7.0 - - - +
183P ILE 3.1 1.0 - - - -
184P SER* 1.3 79.4 + - - +
186P GLY* 1.3 56.6 + - - +
187P ALA 3.7 0.4 - - - -
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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