Contacts of the strand formed by residues 174 - 178 (chain C) in PDB entry 6APL
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 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PHE* 3.5 40.3 - + - +
148C CYS 5.8 0.4 - - - -
149C ILE* 3.9 22.7 - - + -
150C ARG 3.3 2.4 + - - -
151C CYS* 3.3 16.3 - - - -
152C ALA 2.8 24.9 + - - -
172C HIS* 3.7 2.3 - - - +
173C ASP* 1.3 95.0 - - + +
175C VAL* 1.3 66.5 + - - +
176C PHE* 4.3 2.0 - - + -
195C SER* 3.2 25.4 - - - +
196C PHE* 4.1 12.8 - + + -
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ALA* 3.2 7.6 - - + +
154C VAL* 4.1 2.9 - - + -
169C ILE* 3.7 34.8 - - + +
172C HIS* 4.7 1.3 - - + -
174C TYR* 1.3 78.7 - - - +
176C PHE* 1.3 72.6 + - - +
177C ARG* 3.8 21.3 - - - +
193C LYS* 3.2 50.9 - - + +
194C THR* 3.8 0.7 - - - -
195C SER* 2.9 29.7 + - - -
196C PHE 3.2 9.6 + - - +
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Residues in contact with PHE 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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137C LEU* 4.4 12.6 - - + -
138C PHE* 4.4 9.2 - + - -
151C CYS* 4.0 21.5 - - + -
152C ALA 2.7 19.9 + - - +
153C VAL* 3.9 27.1 - - + -
154C VAL* 2.9 28.0 + - - +
174C TYR* 4.7 2.0 - - + -
175C VAL* 1.3 76.3 - - - +
177C ARG* 1.3 64.9 + - - +
178C LEU* 4.6 1.1 - - - -
196C PHE* 3.5 38.6 - + + -
228C ILE* 6.0 0.7 - - + -
309C MSE 3.4 37.0 - - + -
312C THR* 4.5 9.6 - - + -
313C ALA* 3.9 22.4 - - + -
316C THR* 4.6 4.3 - - - -
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Residues in contact with ARG 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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154C VAL* 3.9 25.9 - - + +
169C ILE* 4.0 1.0 - - - +
170C ASP* 3.9 3.0 + - - -
175C VAL* 3.8 11.6 - - + +
176C PHE* 1.3 78.6 - - - +
178C LEU* 1.3 70.6 + - - +
181C ALA* 3.9 19.5 - - + -
183C ILE* 4.1 15.3 - - - +
190C VAL* 2.9 43.4 + - - +
191C GLY* 3.3 21.1 - - - -
192C THR 3.6 1.2 - - - +
193C LYS 2.9 21.0 + - - +
194C THR* 3.0 31.2 + - + +
196C PHE 3.0 10.8 + - - +
197C TYR* 3.2 8.4 - - + -
198C GLY 2.9 23.0 + - - -
220C PRO* 4.7 1.1 - - + -
309C MSE 4.1 1.9 - - - +
337C TYR* 5.3 2.2 + - - -
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Residues in contact with LEU 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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153C VAL* 4.5 8.1 - - + -
154C VAL 3.7 22.3 + - - +
155C GLY* 4.3 7.2 - - - -
156C ASN* 2.8 37.6 + - - +
177C ARG* 1.3 86.9 - - - +
179C ASN* 1.3 67.1 + - + +
181C ALA* 3.5 6.3 + - - +
197C TYR* 3.5 7.7 - - - -
198C GLY 3.1 17.5 - - - +
305C THR* 3.8 11.2 - - + -
306C GLY* 3.8 31.2 - - - +
309C MSE 3.6 27.1 - - + -
325C PHE* 5.3 0.2 - - + -
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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