Contacts of the strand formed by residues 169 - 178 (chain D) in PDB entry 3VXR
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 PHE 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D ASN* 6.5 1.1 - - + -
139D ASP* 4.8 5.6 - - - -
162D LEU* 3.7 0.9 - - - +
163D ASP* 3.5 2.6 + - - -
164D MET* 2.8 53.0 + - + +
167D MET* 3.8 20.6 - - + +
168D ASP* 1.3 77.1 - - - +
170D LYS* 1.3 70.7 + - - +
171D SER* 3.8 15.0 - - - -
139E LYS* 3.7 32.8 - - + -
194E ARG* 3.5 27.6 - - - -
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Residues in contact with LYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 4.4 13.7 + - - +
82D PRO* 3.8 38.3 - - + +
83D GLY 5.9 0.2 - - - +
112D PRO* 4.1 15.0 - - + -
113D ASP 6.0 1.3 - - - +
114D ILE* 3.6 16.4 - - + +
161D VAL* 4.3 9.6 - - + -
162D LEU 3.1 6.7 - - - +
163D ASP* 3.6 34.9 + - + -
168D ASP* 4.5 14.5 + - - -
169D PHE* 1.3 87.6 - - - +
171D SER* 1.3 64.3 + - - +
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Residues in contact with SER 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ILE* 4.2 7.0 - - - -
138D THR* 4.4 2.1 + - - -
139D ASP* 3.5 25.6 - - - -
160D CYS 3.6 0.9 - - - +
161D VAL* 3.5 4.5 - - - +
162D LEU* 3.0 51.4 + - - +
169D PHE* 3.8 6.5 - - - -
170D LYS* 1.3 76.5 - - - +
172D ASN* 1.3 66.4 + - - +
173D SER* 5.2 0.2 + - - -
194E ARG* 3.0 20.5 + - - -
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Residues in contact with ASN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PRO* 3.7 7.8 - - - +
114D ILE* 3.9 6.1 - - - +
138D THR* 3.1 7.1 + - - -
139D ASP 3.0 26.4 + - - +
140D PHE* 3.1 46.8 + - + +
141D ASP 3.6 1.2 + - - -
142D SER* 3.3 35.5 + - - +
159D LYS* 4.7 11.0 - - + +
160D CYS 3.6 4.0 - - - +
161D VAL* 3.5 25.6 - - - +
171D SER* 1.3 74.3 - - - +
173D SER* 1.3 60.8 + - - +
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Residues in contact with SER 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 3.8 10.8 - - - -
137D PHE 3.0 13.0 - - - -
138D THR* 4.0 6.7 - - - -
140D PHE* 3.8 6.5 - - - -
159D LYS* 3.1 3.6 - - - -
160D CYS 2.9 32.7 + - - +
162D LEU* 5.2 6.4 - - - +
171D SER* 5.2 0.6 + - - -
172D ASN* 1.3 77.4 - - - +
174D ALA* 1.3 60.6 + - - +
141E THR* 6.1 0.9 - - - -
170E CYS* 4.2 3.5 - - - -
192E ARG* 2.8 43.7 + - - +
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Residues in contact with ALA 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 3.8 4.7 - - - +
137D PHE* 2.8 33.8 + - + +
140D PHE* 4.2 0.4 - - + -
146D VAL* 3.7 33.2 - - + -
157D THR* 3.7 22.9 - - - +
158D ASP 3.9 3.4 - - - +
173D SER* 1.3 75.2 - - - +
175D VAL* 1.3 64.9 - - - +
189D PHE* 3.8 9.6 - - + -
192E ARG* 3.9 1.3 - - - +
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 4.4 7.6 - - + -
135D CYS 3.4 9.6 - - - +
136D LEU* 4.2 3.4 - - + -
155D TYR 3.7 0.5 - - - +
156D ILE* 3.4 4.5 - - - +
157D THR* 3.0 34.1 + - + +
174D ALA* 1.3 80.6 - - - +
176D ALA* 1.3 66.0 + - - +
177D TRP* 4.0 17.5 - - + -
189D PHE* 3.9 1.8 - - - -
143E VAL* 4.1 31.2 - - + -
145E LEU* 4.9 1.3 - - + -
190E SER* 3.8 16.6 - - - +
192E ARG* 3.5 34.3 - - - +
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 3.7 1.6 - - - +
135D CYS* 2.7 46.1 + - + +
154D VAL* 5.1 2.7 - - + -
155D TYR 3.0 10.8 - - - +
156D ILE* 3.8 13.0 - - + -
175D VAL* 1.3 76.2 - - - +
177D TRP* 1.3 65.2 + - - +
188D ALA* 4.7 9.2 - - + -
189D PHE* 3.4 26.9 - - + -
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Residues in contact with TRP 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D SER 4.3 7.9 - - - +
134D VAL* 4.0 16.6 - - + +
135D CYS* 5.3 3.6 - - - -
154D VAL* 3.6 3.8 - - - +
155D TYR* 3.0 79.7 + + + -
157D THR* 3.9 24.5 - - + -
175D VAL* 4.0 8.5 - - + -
176D ALA* 1.3 80.7 - - - +
178D SER* 1.3 72.1 + - - +
179D ASN* 4.8 6.4 + - - -
145E LEU* 3.5 45.8 - - + +
147E THR* 4.5 7.7 - - + +
176E LEU* 4.0 11.4 - - + -
178E GLU* 5.5 1.5 + - + -
188E ALA* 3.5 33.0 - - + -
189E LEU 5.1 0.4 - - - -
190E SER* 5.3 0.9 - - - -
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Residues in contact with SER 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D SER 4.8 7.8 + - - +
153D ASP 2.7 23.4 + - - -
154D VAL* 3.7 13.3 - - - +
155D TYR* 5.0 0.4 - - - -
177D TRP* 1.3 84.0 - - - +
179D ASN* 1.3 67.7 + - - +
180D LYS* 3.3 25.0 + - - +
183D PHE* 4.5 19.4 - - - +
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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