Contacts of the strand formed by residues 176 - 185 (chain C) in PDB entry 3DGG
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 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLU* 2.6 47.7 + - - +
141C ASN* 3.1 5.9 + - - -
142C PHE* 2.8 53.8 + - + +
143C TYR* 3.9 29.9 - + - -
145C LYS* 3.7 46.8 - - + +
166C TRP* 4.8 1.8 - + + -
167C THR* 3.7 20.2 - - - +
168C ASP* 4.2 1.6 - - - -
169C GLN* 3.6 34.6 + - + -
175C THR* 1.3 75.9 - - - +
177C SER* 1.3 62.7 + - - +
170D HIS* 5.9 0.7 - - - -
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Residues in contact with SER 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU 3.3 5.6 - - - -
140C ASN* 3.4 18.7 + - - -
141C ASN* 2.8 23.2 + - - -
142C PHE* 3.6 3.1 - - - -
166C TRP* 3.4 6.9 - - - -
167C THR* 3.0 37.9 + - - +
176C TYR* 1.3 72.2 + - - +
178C MET* 1.3 62.6 + - - +
170D HIS* 3.6 26.1 + - - -
172D PHE* 3.7 9.9 - - - -
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Residues in contact with MET 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C CYS 4.0 0.3 - - - +
138C PHE* 3.6 2.1 - - - -
139C LEU* 2.8 47.3 + - + +
142C PHE* 4.0 13.0 - - + -
147C ILE* 4.2 4.9 - - - +
149C VAL* 3.3 30.3 - - + -
164C ASN* 3.1 39.0 - - + +
165C SER 3.3 12.6 - - - +
166C TRP* 3.1 46.9 - - + +
177C SER* 1.3 77.5 - - - +
179C SER* 1.3 67.0 + - - +
172D PHE* 3.4 7.6 - - - -
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C VAL* 4.1 2.3 - - - +
137C CYS 3.6 4.2 + - - -
138C PHE* 3.7 16.7 - - - -
163C LEU 3.9 0.8 - - - +
164C ASN* 3.3 6.2 + - - -
165C SER* 2.8 37.1 + - - -
178C MET* 1.3 77.9 - - - +
180C SER* 1.3 60.6 + - - +
181C THR* 3.8 13.7 + - - -
172D PHE* 3.5 30.7 - - - -
184D SER* 4.0 7.9 - - - -
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C VAL* 3.6 1.2 - - - +
137C CYS* 2.8 48.8 + - - -
139C LEU* 5.6 0.9 - - - -
149C VAL* 3.2 29.3 - - - +
151C TRP* 3.0 28.3 + - - -
162C VAL* 3.8 2.4 - - - +
164C ASN* 2.6 23.5 + - - +
178C MET* 4.3 1.1 - - - -
179C SER* 1.3 73.2 + - - +
181C THR* 1.3 61.6 + - - +
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Residues in contact with THR 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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134C SER* 4.3 11.0 - - - +
135C VAL 3.4 8.3 - - - +
136C VAL* 4.1 19.6 - - + +
161C GLY 3.3 5.9 - - - +
162C VAL* 3.4 3.8 - - - -
163C LEU* 3.0 40.8 + - + +
179C SER* 3.8 12.8 + - - -
180C SER* 1.3 74.6 + - - +
182C LEU* 1.3 60.4 + - - +
183C THR* 3.7 17.5 + - - +
147D LEU* 5.1 8.3 - - + +
182D THR* 5.8 4.9 - - + +
184D SER* 4.6 4.7 + - - -
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Residues in contact with LEU 182 (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 VAL* 2.8 43.9 + - + +
151C TRP* 3.9 42.5 - - + +
153C ILE* 3.9 28.7 - - + -
158C ARG* 4.5 11.4 - - + +
160C ASN 4.1 13.0 - - - +
161C GLY 3.6 7.2 - - - +
162C VAL* 4.5 7.9 - - + +
181C THR* 1.3 69.9 - - - +
183C THR* 1.3 74.4 + - - +
184C LEU* 3.3 26.4 - - + +
195C TYR* 4.5 7.0 - - + -
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Residues in contact with THR 183 (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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127C GLN* 6.1 0.2 - - - +
133C ALA 3.9 4.9 - - - +
134C SER* 3.8 17.7 + - - +
158C ARG* 5.3 1.2 + - - -
160C ASN 4.9 0.5 - - - +
161C GLY* 2.9 26.6 + - - +
163C LEU* 5.7 2.6 - - - +
181C THR* 3.7 12.8 + - - +
182C LEU* 1.3 78.9 - - - +
184C LEU* 1.3 70.9 + - - +
149D LYS* 4.8 14.4 - - - +
177D GLN* 4.5 25.7 + - - +
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Residues in contact with LEU 184 (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 GLY* 4.6 0.2 - - - -
133C ALA* 2.7 50.7 + - + +
135C VAL* 4.0 13.7 - - + -
153C ILE* 4.4 9.2 - - + -
158C ARG* 4.4 11.4 - - - +
182C LEU* 3.3 33.0 - - + +
183C THR* 1.3 80.6 - - - +
185C THR* 1.3 73.1 + - - +
188C GLU* 3.4 20.2 - - + +
189C TYR* 4.4 15.5 - - + +
192C HIS* 5.7 1.6 - - + +
195C TYR* 4.2 22.2 - - + +
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Residues in contact with THR 185 (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 GLY 4.4 7.4 - - - +
132C GLY* 5.1 0.9 - - - -
133C ALA* 4.0 0.7 - - - +
184C LEU* 1.3 79.6 - - - +
186C LYS* 1.3 65.4 + - - +
187C ASP* 2.9 24.8 + - - +
188C GLU* 3.1 35.7 + - - +
189C TYR* 3.0 21.0 + - - +
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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