Contacts of the strand formed by residues 170 - 179 (chain C) in PDB entry 2R7D
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 170 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C ALA 5.5 0.7 - - - -
163C GLY 4.3 4.9 + - - -
164C LEU* 3.8 25.7 - - - -
165C GLY 3.3 21.9 + - - -
167C HIS* 3.6 11.9 + - - +
169C VAL* 1.3 78.2 + - - +
171C PRO* 1.3 70.8 - - - +
194C ARG* 3.2 5.2 - - - -
195C VAL* 2.7 45.1 + - - +
197C VAL* 3.6 5.7 - - - +
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Residues in contact with PRO 171 (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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75C PHE* 3.8 43.0 - - + -
81C ARG* 3.3 28.7 - - - +
122C ASP* 4.2 6.2 + - - +
161C LYS 5.2 5.2 - - - +
162C ALA 4.9 3.6 - - - +
164C LEU* 3.6 12.3 - - - +
169C VAL 4.4 2.0 - - - +
170C SER* 1.3 89.5 - - - +
172C ALA* 1.3 63.0 + - - +
193C THR 3.4 6.7 - - - +
194C ARG* 4.3 16.8 - - - +
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Residues in contact with ALA 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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81C ARG* 2.9 13.8 + - - +
119C HIS* 4.1 7.2 - - + -
120C VAL 3.2 26.0 - - - +
122C ASP* 3.8 5.4 - - - -
164C LEU* 4.1 9.6 - - + -
171C PRO* 1.3 77.1 - - - +
173C LEU* 1.3 58.6 + - - +
174C SER* 4.1 3.1 - - - +
192C LEU* 3.5 1.0 - - - -
193C THR* 2.8 46.0 + - - +
195C VAL* 4.6 5.8 - - + -
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Residues in contact with LEU 173 (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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120C VAL* 3.0 31.6 + - - +
122C ASP* 3.8 13.8 - - - +
172C ALA* 1.3 71.2 - - - +
174C SER* 1.3 62.6 + - - +
175C ILE* 4.3 11.4 - - + -
190C VAL* 3.6 26.9 - - + -
191C LEU 3.8 4.7 - - - +
192C LEU* 4.5 9.9 - - + -
351C HIS* 3.6 45.3 - - + +
354C LEU* 4.1 21.5 - - + -
355C ARG* 4.0 22.9 - - + -
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Residues in contact with SER 174 (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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117C TRP* 3.9 12.3 - - - -
118C VAL 3.5 5.8 - - - -
119C HIS* 2.7 29.5 + - - +
172C ALA* 3.8 0.4 - - - +
173C LEU* 1.3 76.2 - - - +
175C ILE* 1.3 65.0 + - - +
189C ASP 3.7 0.2 - - - +
190C VAL* 3.1 7.6 - - - +
191C LEU* 2.8 36.1 + - - +
193C THR* 2.6 38.4 + - - -
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Residues in contact with ILE 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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116C LEU 3.7 0.9 - - - +
117C TRP* 3.7 2.2 - - - -
118C VAL* 2.9 43.6 + - - +
120C VAL* 4.1 19.7 - - + -
173C LEU* 4.3 13.0 - - + -
174C SER* 1.3 79.0 - - - +
176C CYS* 1.3 62.8 + - - +
177C LEU* 3.9 18.8 - - + +
188C VAL* 4.1 14.1 - - + -
189C ASP 3.2 9.4 - - - +
190C VAL* 4.3 10.5 - - + -
273C ALA* 3.8 31.0 - - + +
276C GLY 4.4 0.7 - - - -
277C THR* 3.5 23.3 - - - +
338C ALA* 5.3 6.5 - - + +
339C THR* 5.4 0.2 - - + -
354C LEU* 5.8 0.9 - - + -
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Residues in contact with CYS 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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115C ARG* 4.2 17.5 - - + -
116C LEU 3.1 8.1 - - - +
117C TRP* 3.5 41.1 - - + -
175C ILE* 1.3 74.3 - - - +
177C LEU* 1.3 62.9 + - - +
178C ASP* 5.1 0.9 - - - -
187C ALA 3.8 0.5 - - - +
188C VAL* 3.3 5.2 - - - +
189C ASP* 2.8 70.5 + - - +
191C LEU* 4.3 1.8 - - - -
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Residues in contact with LEU 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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114C THR 3.4 2.3 - - - +
115C ARG* 3.2 1.0 - - - -
116C LEU* 2.7 54.1 + - + +
118C VAL* 5.2 1.6 - - + -
175C ILE* 3.9 20.4 - - + +
176C CYS* 1.3 81.2 - - - +
178C ASP* 1.3 64.1 + - - +
179C LEU* 3.5 20.8 + - + +
185C ALA* 4.8 0.7 - - + -
187C ALA 3.4 5.8 - - - +
188C VAL* 3.9 21.8 - - + -
272C LEU* 3.5 35.2 - - + +
273C ALA* 4.6 2.2 - - - +
275C TRP* 3.9 25.6 - - + -
276C GLY* 4.2 2.2 - - - -
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Residues in contact with ASP 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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109C LEU* 3.4 22.7 - - + +
113C LEU* 4.1 8.1 - - + -
114C THR 3.5 4.7 - - - -
115C ARG* 2.7 43.8 + - - +
176C CYS* 5.0 0.7 - - - -
177C LEU* 1.3 72.6 + - - +
179C LEU* 1.3 60.1 + - - +
184C ASN 3.5 0.5 - - - +
185C ALA* 3.4 1.4 - - - -
186C GLU* 2.8 36.7 + - + +
187C ALA* 2.9 37.7 + - + +
189C ASP* 4.7 3.7 - - - +
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Residues in contact with LEU 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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112C GLY 4.0 0.2 - - - +
113C LEU* 3.3 6.4 - - - +
114C THR* 2.7 44.5 + - - +
116C LEU* 4.4 17.0 - - + -
177C LEU* 4.1 21.3 - - + +
178C ASP* 1.3 71.6 - - - +
180C ASP* 1.3 65.0 + - - +
183C GLY* 3.9 24.0 - - - +
184C ASN 3.2 9.4 - - - +
185C ALA* 3.9 18.2 - - + -
222C LEU* 4.3 27.9 - - + +
226C SER* 6.2 0.9 - - - -
272C LEU* 4.3 26.7 - - + -
275C TRP* 4.8 4.7 - - + -
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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