Contacts of the strand formed by residues 180 - 183 (chain F) in PDB entry 1C9T
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 MET 180 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98F THR* 3.7 15.9 - - - +
99F LEU 3.5 23.1 - - - +
100F ASN* 3.8 6.7 - - - -
165F ASP* 4.9 4.3 - - - +
175F GLN 3.8 11.4 - - - +
176F ILE* 4.3 11.6 - - + +
177F THR* 3.1 52.7 + - + +
178F SER 4.3 4.7 - - - +
179F ASN* 1.3 85.1 - - + +
181F PHE* 1.3 66.1 + - - +
215F TRP* 3.4 36.3 - - + +
227F VAL* 3.9 10.8 - - + -
228F TYR 3.4 8.1 - - - +
229F THR* 5.5 0.7 - - - -
230F LYS* 4.3 6.2 + - - +
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Residues in contact with PHE 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F ILE* 3.8 33.2 - - + -
163F LEU 5.6 1.6 - - - +
165F ASP* 6.0 1.8 - - - +
168F CYS* 4.0 7.4 - - - -
180F MET* 1.3 76.5 - - - +
182F CYS* 1.3 69.7 + - - +
183F ALA* 4.1 11.7 - - + -
199F VAL* 4.0 13.2 - - + -
210F GLN* 3.3 30.3 - - + -
211F GLY* 3.5 24.7 - - - -
227F VAL* 3.6 0.8 - - - -
228F TYR* 2.8 54.3 + - + -
229F THR 3.6 4.0 - - - -
230F LYS* 3.9 25.1 - - + -
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Residues in contact with CYS 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F ILE 3.7 0.9 - - - -
163F LEU* 2.8 46.1 + - + +
168F CYS* 2.0 60.3 - - + +
172F TYR* 4.1 22.2 - - - -
181F PHE* 1.3 80.4 - - - +
183F ALA* 1.3 60.5 + - - +
225F PRO* 4.1 6.3 - - + -
226F GLY 3.2 7.4 - - - +
227F VAL* 4.1 9.2 - - - -
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Residues in contact with ALA 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F CYS* 6.2 1.1 - - + -
138F ILE* 4.6 9.4 - - + -
160F ALA* 4.8 2.7 - - + +
161F PRO 3.1 19.3 - - - +
162F ILE* 4.4 1.6 - - + -
163F LEU* 3.9 5.6 - - - -
181F PHE* 4.1 12.8 - - + -
182F CYS* 1.3 75.9 - - - +
184F GLY* 1.3 58.6 + - - +
189F ASP* 4.8 0.7 - - - +
199F VAL* 5.5 3.6 - - + -
225F PRO* 3.9 1.6 - - - +
226F GLY 3.0 28.0 + - - +
228F TYR* 3.6 28.5 + - + -
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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