Contacts of the strand formed by residues 166 - 175 (chain D) in PDB entry 4NQD
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 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D ILE* 6.6 0.2 - - + -
113D ASN* 5.9 4.3 - - + -
136D ASP* 4.5 7.9 - - + -
159D LEU* 3.9 0.6 - - + +
160D ASP* 3.3 3.9 + - - +
161D MET* 2.7 53.0 + - + +
164D MET* 4.0 21.8 - - + +
165D ASP* 1.3 76.6 - - - +
167D LYS* 1.3 71.6 + - - +
168D SER* 3.7 15.5 - - - -
141E LYS* 3.7 34.8 - - + +
196E ARG* 3.4 28.3 - - - -
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Residues in contact with LYS 167 (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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14D GLU* 4.0 20.6 + - - +
80D MET* 3.5 34.8 - - + +
109D PRO* 4.2 20.2 - - + -
110D ASP 5.3 5.1 - - - +
111D ILE* 3.7 16.5 - - + +
158D VAL* 4.7 4.7 - - + -
159D LEU 3.3 8.7 - - - +
160D ASP* 3.8 32.9 + - + +
162D ARG* 4.2 8.1 - - - +
165D ASP* 4.3 7.6 + - - -
166D PHE* 1.3 85.5 - - - +
168D SER* 1.3 62.6 + - - +
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Residues in contact with SER 168 (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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111D ILE* 4.1 7.4 - - - +
135D THR* 4.4 2.6 + - - -
136D ASP* 3.4 25.3 + - - -
157D CYS 3.5 1.2 - - - +
158D VAL* 3.5 5.4 - - - +
159D LEU* 2.9 49.2 + - - +
166D PHE* 3.7 9.9 - - - -
167D LYS* 1.3 74.7 - - - +
169D ASN* 1.3 63.4 + - - +
170D SER* 5.2 1.0 + - - -
196E ARG* 3.1 19.9 + - - -
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Residues in contact with ASN 169 (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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109D PRO* 3.6 5.3 - - - +
111D ILE* 3.7 8.9 - - - +
135D THR* 3.3 4.3 + - - -
136D ASP* 3.0 26.6 + - - +
137D PHE* 3.0 46.0 + - + +
138D ASP 3.8 0.8 - - - -
139D SER* 3.3 29.1 + - - +
156D LYS* 3.0 26.3 + - + +
157D CYS 3.3 5.2 - - - +
158D VAL* 3.3 19.8 - - - +
168D SER* 1.3 73.8 - - - +
170D SER* 1.3 60.6 + - - +
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Residues in contact with SER 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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133D LEU* 3.8 13.5 - - - -
134D PHE 3.2 12.8 - - - -
135D THR* 3.7 11.9 - - - -
137D PHE* 3.9 4.9 - - - -
156D LYS* 3.4 3.3 - - - -
157D CYS 2.8 32.1 + - - -
159D LEU* 5.3 4.7 - - - +
168D SER* 5.2 2.0 + - - -
169D ASN* 1.3 76.4 - - - +
171D ALA* 1.3 61.6 + - - +
143E THR* 5.8 0.6 - - - +
194E ARG* 2.8 39.4 + - - +
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Residues in contact with ALA 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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133D LEU* 3.6 4.0 - - - +
134D PHE* 3.0 32.6 + - + +
137D PHE* 4.8 0.4 - - + -
143D VAL* 3.7 31.6 - - + -
154D THR 3.6 17.9 - - - +
155D ASP 4.2 4.0 - - - +
170D SER* 1.3 75.7 - - - +
172D VAL* 1.3 62.4 + - - +
186D PHE* 3.6 11.3 - - + -
194E ARG* 3.7 6.7 - - - +
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Residues in contact with VAL 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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131D VAL* 3.8 24.0 - - + -
132D CYS 3.4 4.5 - - - +
133D LEU* 4.3 7.0 - - + -
152D TYR 3.9 0.7 - - - +
153D ILE* 3.3 4.7 - - - +
154D THR* 2.9 39.5 + - - +
171D ALA* 1.3 76.4 - - - +
173D ALA* 1.3 62.8 - - - +
174D TRP* 3.6 23.4 - - + -
186D PHE* 4.0 1.3 - - - -
145E VAL* 4.0 31.0 - - + -
147E LEU* 4.1 2.2 - - + -
192E SER* 4.0 9.6 - - - +
194E ARG* 4.0 21.5 - - + +
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Residues in contact with ALA 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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130D SER 3.9 0.2 - - - +
131D VAL* 3.5 1.2 - - - +
132D CYS* 2.7 38.8 + - - +
152D TYR 3.1 9.6 - - - +
153D ILE* 3.8 16.2 - - + -
172D VAL* 1.3 75.4 - - - +
174D TRP* 1.3 62.0 + - - +
180D PHE* 4.0 6.0 - - + -
185D ALA* 3.9 21.8 - - + -
186D PHE* 3.5 21.3 - - + -
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Residues in contact with TRP 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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129D LYS* 3.7 34.8 - - + +
130D SER 3.2 13.9 - - - +
131D VAL* 4.0 15.9 - - + -
151D VAL* 3.6 2.6 - - - +
152D TYR* 2.9 77.4 + + + -
154D THR* 3.6 32.3 - - + -
172D VAL* 3.6 21.1 - - + -
173D ALA* 1.3 74.8 - - - +
175D SER* 1.3 66.8 + - - +
180D PHE* 3.9 4.5 - - - -
147E LEU* 3.6 26.7 - - + -
149E THR* 4.0 8.8 - - + +
178E LEU* 4.2 1.8 - - + -
180E GLU* 5.6 0.6 + - - -
190E ALA* 3.5 30.5 - - + -
191E LEU 5.1 1.6 - - - -
192E SER* 4.7 2.0 - - - -
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Residues in contact with SER 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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129D LYS* 4.2 5.4 - - - -
130D SER* 2.8 36.1 + - - +
150D ASP 2.6 25.9 + - - -
151D VAL* 3.9 2.7 - - - -
152D TYR* 5.0 2.7 - - - -
174D TRP* 1.3 81.2 - - - +
176D ASN* 1.3 59.5 + - - +
177D LYS* 3.2 21.8 + - - +
180D PHE* 3.5 30.2 - - - +
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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