Contacts of the strand formed by residues 176 - 185 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLU* 4.1 9.5 - - - +
109A LEU 5.3 0.2 + - - -
141A ASN 3.1 5.4 + - - -
142A PHE* 2.8 60.2 + - + +
143A TYR* 4.0 23.6 - + - -
145A LYS* 3.5 60.1 + - + -
167A THR* 3.9 20.9 - - - +
168A ASP* 4.4 1.1 - - - -
169A GLN* 3.6 50.2 + - + +
175A THR* 1.3 75.6 - - - +
177A SER* 1.3 63.2 + - - +
170B HIS* 5.9 0.2 - - - -
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU 3.5 6.1 - - - -
140A ASN* 3.6 14.5 - - - -
141A ASN* 3.0 21.0 + - - -
142A PHE* 3.8 4.6 - - - -
166A TRP* 3.6 4.3 - - - +
167A THR* 3.0 38.1 + - - +
176A TYR* 1.3 72.0 + - - +
178A MET* 1.3 63.5 + - - +
170B HIS* 3.4 28.8 + - - -
172B PHE* 3.7 11.0 - - - -
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PHE* 3.7 2.1 - - - -
139A LEU* 2.7 42.7 + - + +
142A PHE* 3.9 11.4 - - + -
147A ILE* 3.6 17.5 - - + +
149A VAL* 3.5 35.9 - - + +
164A ASN* 3.4 36.8 - - - +
165A SER 3.3 12.1 - - - +
166A TRP* 3.2 38.8 - - + +
177A SER* 1.3 79.0 - - - +
179A SER* 1.3 64.7 + - - +
180A SER* 4.8 0.9 - - - -
172B PHE* 3.4 9.3 - - - -
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A VAL* 5.4 0.9 - - - -
137A CYS 3.4 5.2 - - - -
138A PHE* 3.8 16.8 - - - -
139A LEU* 4.8 0.2 - - - -
163A LEU 3.9 0.7 + - - +
164A ASN* 3.3 4.0 - - - -
165A SER* 2.9 40.2 + - - +
178A MET* 1.3 80.2 - - - +
180A SER* 1.3 62.2 + - - +
181A THR* 4.9 4.1 + - - -
172B PHE* 3.5 15.8 - - - +
184B SER* 3.4 24.8 + - - -
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A VAL* 3.7 0.2 - - - -
137A CYS* 2.8 42.0 + - - +
139A LEU* 4.4 4.7 - - - +
149A VAL* 3.8 22.9 - - - +
151A TRP* 3.0 32.0 + - - -
162A VAL* 3.8 3.8 - - - +
163A LEU 3.5 3.1 - - - -
164A ASN* 2.5 22.5 + - - -
178A MET* 4.8 0.4 - - - -
179A SER* 1.3 73.8 - - - +
181A THR* 1.3 63.6 + - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER* 3.8 25.8 - - - -
135A VAL 3.4 9.4 - - - +
136A VAL* 4.0 19.5 - - + +
151A TRP* 4.5 2.0 - - - -
161A GLY 3.2 5.4 - - - +
162A VAL* 3.3 1.8 - - - -
163A LEU* 2.8 48.6 + - + +
179A SER* 4.9 3.3 + - - -
180A SER* 1.3 76.6 + - - +
182A LEU* 1.3 60.3 + - - +
183A THR* 3.8 10.7 + - - +
147B LEU* 5.0 10.0 - - + +
149B LYS* 6.2 0.2 - - - +
182B THR* 5.7 6.8 - - + +
184B SER* 4.8 7.3 + - - -
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ALA 3.7 1.9 - - - +
134A SER* 3.4 0.5 - - - -
135A VAL* 2.8 39.8 + - + +
151A TRP* 3.6 49.0 - - + +
153A ILE* 4.2 27.1 - - + -
158A ARG* 4.9 7.6 - - + -
160A ASN 3.2 28.0 - - - +
161A GLY 3.4 1.8 - - - +
162A VAL* 3.6 11.2 - - + -
181A THR* 1.3 70.8 - - - +
183A THR* 1.3 62.1 + - - +
184A LEU* 3.5 19.0 - - + +
195A TYR* 4.8 6.1 - - + -
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY* 6.4 0.2 - - - -
133A ALA 3.5 5.4 - - - +
134A SER* 3.1 19.3 + - - +
160A ASN 4.7 0.7 - - - +
161A GLY* 2.8 30.9 + - - -
163A LEU* 5.6 6.1 - - - +
181A THR* 4.0 9.4 + - - +
182A LEU* 1.3 72.4 - - - +
184A LEU* 1.3 74.4 + - - +
149B LYS* 3.8 24.9 + - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY* 3.9 1.6 - - - -
133A ALA* 2.8 34.3 + - + +
135A VAL* 4.8 7.6 - - + -
153A ILE* 4.5 9.9 - - + -
182A LEU* 3.5 37.9 - - + +
183A THR* 1.3 86.2 - - - +
185A THR* 1.3 66.0 + - - +
188A GLU* 3.3 21.1 - - + +
189A TYR* 3.7 31.6 - - + +
192A HIS* 5.0 3.1 - - + +
195A TYR* 3.9 15.9 - - + +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLY 3.9 9.4 - - - +
132A GLY* 4.7 0.7 - - - -
133A ALA* 4.0 0.9 - - - -
184A LEU* 1.3 76.1 - - - +
186A LYS* 1.3 64.6 + - - +
187A ASP* 3.7 5.2 + - - +
188A GLU* 2.9 49.0 + - - +
189A TYR* 2.9 22.3 + - - +
454A MG 3.8 5.9 - - - -
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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