Contacts of the strand formed by residues 175 - 181 (chain C) in PDB entry 3E2A
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 175 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C GLU 2.8 10.1 + - - -
92C HIS* 2.6 40.5 + - - -
93C ILE 3.0 24.6 + - - -
173C LYS* 5.8 4.5 - - - +
174C LEU* 1.3 75.9 - - - +
176C LEU* 1.3 64.9 + - - +
177C HIS* 2.7 16.1 + - - -
194C MET* 4.4 2.7 - - - -
195C ALA 3.2 3.6 - - - -
196C THR* 3.7 22.0 - - - -
1E MET 6.2 0.4 - - - -
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Residues in contact with LEU 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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93C ILE* 3.5 20.4 - - + +
155C VAL* 3.9 22.0 - - + +
158C LEU* 3.9 25.8 - - + -
159C GLY* 3.5 37.5 - - - +
164C VAL* 4.3 6.3 - - + -
168C TRP* 3.9 15.3 - - + -
174C LEU* 4.3 11.9 - - + -
175C SER* 1.3 79.2 - - - +
177C HIS* 1.3 65.0 + - - +
194C MET* 3.3 11.3 - - - +
195C ALA* 2.8 37.9 + - + +
201C LEU* 4.4 0.2 - - + -
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Residues in contact with HIS 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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92C HIS* 3.0 12.5 + + + -
93C ILE 2.9 21.7 + - - +
94C ILE* 3.6 8.2 - - + -
95C ILE* 2.8 29.7 + - - +
155C VAL* 3.7 11.6 - - - +
158C LEU* 5.6 0.3 - - - +
175C SER* 2.7 37.1 + - - -
176C LEU* 1.3 79.9 + - - +
178C GLY* 1.3 53.9 + - - +
179C TRP* 3.8 29.5 + + + +
193C VAL 4.0 4.5 - - - -
194C MET* 3.9 18.6 - - + +
1E MET 4.8 4.3 - - - -
4E ILE* 3.6 32.7 - - + +
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Residues in contact with GLY 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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95C ILE 3.2 7.4 - - - -
151C VAL* 3.5 12.3 - - - -
155C VAL* 3.6 18.4 - - - -
177C HIS* 1.3 76.2 - - - +
179C TRP* 1.3 61.9 + - - -
190C ASP* 3.2 7.7 + - - +
191C GLN* 3.1 27.9 + - - +
192C GLY 4.4 0.3 + - - -
193C VAL 3.7 9.8 + - - +
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Residues in contact with TRP 179 (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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39C TRP* 3.9 8.3 - + - -
94C ILE* 3.4 44.6 - - + -
95C ILE 2.9 7.9 + - - +
96C CYS* 3.3 5.2 - - + -
97C GLY 2.8 23.4 + - - -
151C VAL* 3.5 6.4 - - - +
177C HIS* 3.8 26.2 + + + +
178C GLY* 1.3 83.4 - - - -
180C VAL* 1.3 64.1 + - - +
188C LEU* 4.0 28.5 - - + -
189C VAL 3.3 11.7 - - - +
190C ASP* 3.7 25.7 + - + -
191C GLN* 4.5 0.7 - - - -
4E ILE* 3.9 19.5 - - + +
7E LEU* 3.7 29.4 - - + -
8E PHE* 3.4 31.1 - + - -
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Residues in contact with VAL 180 (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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96C CYS* 4.5 1.3 - - - -
97C GLY 3.5 6.5 - - - -
98C HIS* 3.9 12.6 - - - +
99C THR* 4.1 17.3 - - + +
144C ASP* 5.4 0.4 - - - +
147C THR* 4.4 7.2 - - + +
148C LYS* 4.3 20.9 - - + -
151C VAL* 3.8 18.8 - - + -
179C TRP* 1.3 79.2 - - - +
181C PHE* 1.3 74.0 + - - +
182C ASP* 3.7 2.7 + - + +
187C PHE 3.7 0.3 - - - +
188C LEU* 3.6 2.3 - - - -
189C VAL* 2.9 33.9 + - + +
191C GLN* 3.9 25.8 - - + +
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Residues in contact with PHE 181 (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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47C VAL* 3.8 28.0 - - + -
52C LEU* 3.4 33.0 - - + -
96C CYS* 3.9 13.3 - - - -
97C GLY 2.9 16.0 + - - +
98C HIS* 3.2 6.7 - - + +
99C THR 3.2 23.7 + - - -
180C VAL* 1.3 74.9 - - - +
182C ASP* 1.3 59.6 + - - +
183C VAL* 3.7 21.0 + - - -
186C GLY* 3.2 41.1 - - - -
187C PHE 3.9 2.5 - - - -
188C LEU* 4.0 9.9 - - + -
232C SO4 3.6 20.4 - - - -
14E TRP* 3.9 18.2 - + - -
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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