Contacts of the strand formed by residues 171 - 178 (chain C) in PDB entry 4CQM
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 ILE 171 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C MET* 4.4 5.2 - - - -
122C MET* 3.5 45.3 - - + +
123C ILE* 3.9 10.5 - - + +
127C GLY 3.8 1.3 - - - -
128C GLY* 3.3 24.2 - - - +
130C ILE* 4.6 5.2 - - + -
163C ALA 4.4 2.6 - - - +
166C VAL* 3.3 58.8 + - + +
167C ALA* 4.0 7.5 + - - -
169C LYS* 3.2 15.7 - - + +
170C LYS* 1.3 79.0 - - - +
172C ARG* 1.3 68.3 + - - +
173C VAL* 4.0 6.8 + - + -
223C THR* 4.5 1.0 + - - -
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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
----------------------------------------------------------
79C PHE* 5.0 0.6 - - - -
128C GLY 3.0 10.0 + - - +
129C SER* 3.1 16.0 + - - -
130C ILE* 2.6 35.7 + - - +
170C LYS 5.2 2.7 - - - +
171C ILE* 1.3 76.6 - - - +
173C VAL* 1.3 56.6 + - - +
174C ASN* 3.9 3.3 - - - +
216C LEU 2.7 23.0 + - - -
217C LEU 2.5 31.1 + - - -
218C GLU 4.0 4.0 - - - +
219C SER 2.8 18.0 + - - -
220C PRO* 3.4 26.4 + - - +
222C ILE 3.1 28.8 + - - +
223C THR* 3.7 15.3 - - + -
224D MET* 4.7 11.4 - - + -
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ILE* 3.3 32.1 - - + +
132C ASN* 3.9 14.8 - - - +
159C SER* 3.7 38.7 - - - +
162C LEU* 4.0 23.8 - - + -
163C ALA* 3.7 12.4 - - + +
166C VAL* 4.5 9.4 - - + -
171C ILE* 4.0 1.5 + - + -
172C ARG* 1.3 77.4 - - - +
174C ASN* 1.3 57.5 + - - +
223C THR* 3.4 6.3 + - - -
224C GLY* 2.8 30.8 + - - -
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Residues in contact with ASN 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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129C SER* 5.4 0.6 + - - -
130C ILE 2.7 15.2 + - - +
131C VAL* 3.3 7.1 - - + +
132C ASN* 2.8 27.4 + - - +
159C SER* 5.2 0.2 - - - -
172C ARG* 3.9 14.8 - - - +
173C VAL* 1.3 76.5 - - - +
175C VAL* 1.3 69.5 - - - +
216C LEU* 3.7 20.5 + - + -
222C ILE* 2.9 39.0 + - - +
223C THR* 3.2 9.3 - - - +
224C GLY* 3.0 5.8 + - - +
225C HIS 2.8 32.6 + - - +
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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
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132C ASN* 3.3 18.4 - - + +
134C GLY* 4.4 8.1 - - - +
135C SER 5.7 0.2 - - - +
152C LYS 6.1 0.2 - - - +
155C LEU* 3.9 13.9 - - + +
156C VAL* 4.5 13.0 - - + +
159C SER* 3.3 32.5 - - - +
160C ARG* 6.4 0.4 - - + -
174C ASN* 1.3 79.7 - - - +
176C VAL* 1.3 72.9 + - - +
177C ALA* 4.9 1.6 - - + -
216C LEU* 3.9 2.4 - - - +
224C GLY 6.5 0.4 - - - -
225C HIS 3.2 6.4 + - - +
226C VAL* 3.2 27.9 - - + -
227C LEU* 2.8 26.9 + - - -
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Residues in contact with VAL 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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131C VAL* 3.7 23.7 - - + +
132C ASN 3.3 6.3 + - - -
133C VAL* 3.6 5.9 - - + -
134C GLY* 2.7 32.1 + - - -
175C VAL* 1.3 73.8 - - - +
177C ALA* 1.3 59.6 + - - +
178C PRO* 3.2 6.8 - - + +
209C VAL* 3.9 19.1 - - + -
212C ALA* 4.4 7.0 - - + -
213C VAL* 3.7 23.6 - - + +
216C LEU* 3.7 20.0 - - + -
227C LEU* 3.6 6.7 - - + +
229C VAL* 3.9 24.7 - - + -
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Residues in contact with ALA 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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135C SER* 3.6 26.5 - - - +
136C ILE* 3.7 8.3 + - + +
139C LEU* 4.2 5.2 - - + -
175C VAL* 4.0 2.4 + - + -
176C VAL* 1.3 72.3 - - - +
178C PRO* 1.3 66.8 - - - +
226C VAL* 3.8 23.6 - - + -
227C LEU 2.9 12.4 + - - +
228C VAL* 3.8 11.5 - - + +
229C VAL* 3.4 18.1 + - - +
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Residues in contact with PRO 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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14C ILE* 3.6 25.1 - - + -
133C VAL* 4.1 3.6 - - + -
134C GLY 3.2 19.5 - - - +
135C SER* 3.5 6.6 + - - +
136C ILE* 3.0 20.8 + - - -
176C VAL* 3.2 12.8 - - + +
177C ALA* 1.3 86.2 - - - +
179C GLY* 1.3 63.8 + - - +
181C VAL* 3.9 23.1 - - + -
209C VAL* 3.7 20.4 - - + -
229C VAL* 3.3 11.2 - - + +
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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