Contacts of the strand formed by residues 171 - 178 (chain C) in PDB entry 2B5L
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 HIS 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C GLU* 5.5 0.2 - - - +
148C PRO* 3.5 24.6 - - - +
151C ASN* 5.1 0.7 + - - -
170C PHE* 1.3 93.6 - - - +
172C ARG* 1.3 60.7 + - - +
173C ARG 4.1 0.6 + - - -
190C CYS* 3.6 19.0 - - + -
191C ASN 3.1 13.7 - - - +
192C PRO* 4.2 10.8 - - + +
193C SER* 4.3 2.9 - - - -
212C PRO* 2.7 35.7 + - + +
213C VAL 3.6 23.8 - - - -
214C THR* 3.8 10.8 - - - -
215C CYS* 3.6 13.0 - - + +
218C CYS* 4.1 4.7 - - - -
3002C ZN 3.0 22.0 - - - -
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Residues in contact with ARG 172 (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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145C ILE* 3.4 25.6 - - + -
146C GLU 4.2 4.9 - - - +
147C GLU* 3.4 33.9 + - + +
163C ARG* 3.7 11.5 - - - +
171C HIS* 1.3 73.4 - - - +
173C ARG* 1.3 61.6 + - - +
174C GLU* 2.7 38.7 + - - +
190C CYS* 4.7 1.1 - - - -
191C ASN* 2.7 53.5 + - - +
192C PRO 3.4 13.8 + - - -
193C SER* 3.9 7.5 + - - +
195C SER* 2.6 36.8 + - - -
196C PRO 3.5 17.2 + - - -
197C ILE* 3.4 19.0 - - - +
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Residues in contact with ARG 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C THR* 4.3 0.8 + - - -
144C PHE 3.8 0.3 - - - +
145C ILE* 3.2 16.3 - - - +
146C GLU* 3.4 32.8 + - + +
148C PRO* 5.2 2.9 - - + +
171C HIS 4.1 0.8 + - - -
172C ARG* 1.3 72.1 - - - +
174C GLU* 1.3 61.8 + - - +
175C TYR* 3.8 27.0 + - + +
188C GLU* 3.1 42.9 + - - +
189C TRP* 3.3 27.7 - - - +
190C CYS* 3.5 22.0 - - - +
217C GLU* 3.6 29.9 + - - +
221C ASP* 3.5 24.4 + - - -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 5.4 0.3 - - - +
143C ARG* 2.4 32.9 + - - -
144C PHE 3.5 2.7 - - - -
145C ILE* 3.0 21.1 - - - +
172C ARG* 2.7 34.2 + - - +
173C ARG* 1.3 74.6 - - - +
175C TYR* 1.3 69.6 + - - +
188C GLU* 3.3 6.2 - - - +
189C TRP* 2.7 63.5 + - + +
191C ASN* 3.1 27.9 + - + +
197C ILE* 5.0 2.8 - - - +
198C THR 5.2 1.4 + - - +
204C PHE* 6.1 0.4 - - - -
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Residues in contact with TYR 175 (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* 5.3 1.6 - - + -
128C LYS* 3.4 26.8 + - + +
129C GLY* 4.3 13.7 - - - -
132C LEU* 3.6 32.8 - - + -
142C THR 3.4 0.3 - - - +
143C ARG* 3.1 15.2 + - - +
144C PHE* 2.9 53.2 + - + +
145C ILE 4.7 0.4 - - - -
146C GLU* 3.7 16.4 + - + -
173C ARG* 3.8 25.6 + - + +
174C GLU* 1.3 76.1 - - - +
176C SER* 1.3 60.0 + - - +
177C ILE* 4.0 7.4 - - + -
186C VAL* 4.3 11.7 - - + -
187C THR 3.7 2.7 - - - -
188C GLU* 2.9 40.9 + - + -
189C TRP* 4.1 1.3 - - - -
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Residues in contact with SER 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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98C ILE* 4.9 5.7 + - - +
99C PRO 5.7 0.2 - - - -
101C PRO* 3.7 19.1 - - - +
142C THR 3.5 2.9 - - - -
143C ARG* 3.9 6.6 - - - -
175C TYR* 1.3 71.2 - - - +
177C ILE* 1.3 64.2 + - - +
186C VAL* 3.1 7.1 - - - +
187C THR* 2.9 39.5 + - - -
189C TRP* 4.0 7.8 - - - -
201C ALA* 3.6 26.2 - - - +
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Residues in contact with ILE 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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101C PRO* 4.2 5.7 - - - +
132C LEU* 4.9 4.0 - - + +
133C ALA* 4.5 11.2 - - - +
136C GLY* 5.2 0.7 - - - -
141C MET 4.7 1.3 - - - +
142C THR* 3.0 53.6 + - - +
144C PHE* 3.6 26.5 - - + -
175C TYR* 3.9 11.4 - - + +
176C SER* 1.3 81.5 - - - +
178C GLY* 1.3 60.8 + - - +
179C TRP* 3.3 25.6 - - + -
184C VAL* 3.5 17.7 - - + -
185C LYS 3.3 10.1 - - - +
186C VAL* 3.8 16.6 - - + -
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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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100C ASN* 5.2 1.3 - - - -
101C PRO* 4.0 7.8 - - - +
102C LEU* 3.7 22.7 - - - -
177C ILE* 1.3 73.5 - - - +
179C TRP* 1.3 74.1 + - - +
184C VAL* 3.5 5.9 - - - +
185C LYS 2.8 33.4 + - - -
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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