Contacts of the strand formed by residues 172 - 181 (chain D) in PDB entry 4WFH
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 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D LYS* 6.0 5.4 - - - -
104D GLU* 3.1 37.6 + - - +
137D ASN* 3.0 6.4 + - - -
138D PHE* 2.8 53.3 + - + +
139D TYR* 3.7 29.4 - + - -
141D LYS* 3.8 48.1 - - + +
162D TRP* 5.9 1.6 - - + -
163D THR* 3.9 14.1 - - - -
164D ASP* 4.2 1.3 - - - -
165D GLN* 3.5 42.9 - - + +
171D THR* 1.3 75.6 - - - +
173D SER* 1.3 65.4 + - - +
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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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135D LEU 3.3 12.8 - - - -
136D ASN* 3.7 14.2 - - - -
137D ASN* 3.0 13.7 + - - -
138D PHE* 3.6 4.7 - - - -
162D TRP* 3.5 3.3 - - - +
163D THR* 3.0 40.0 + - - +
171D THR* 4.8 0.9 + - - -
172D TYR* 1.3 79.2 + - - +
174D MET* 1.3 63.5 + - - +
167E HIS* 3.7 21.5 + - - -
169E PHE* 3.7 10.7 - - - -
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Residues in contact with MET 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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134D PHE* 3.7 1.2 - - - -
135D LEU* 2.8 50.9 + - + +
138D PHE* 3.9 2.4 - - + -
143D ILE* 4.2 16.8 - - + +
145D VAL* 4.1 14.6 - - + -
160D ASN* 3.3 36.3 - - + +
161D SER 3.1 13.9 - - - +
162D TRP* 3.5 35.9 - - + -
173D SER* 1.3 75.3 - - - +
175D SER* 1.3 81.8 + - - +
176D SER* 3.8 7.9 - - - -
169E PHE* 3.2 10.5 - - - -
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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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132D VAL* 5.3 0.4 - - - -
133D CYS 3.3 4.9 - - - -
134D PHE* 4.0 16.2 - - - -
159D LEU 4.8 1.2 + - - -
160D ASN* 3.4 1.6 - - - -
161D SER* 2.9 41.1 + - - -
174D MET* 1.3 85.5 - - - +
176D SER* 1.3 59.4 + - - +
177D THR* 4.3 9.0 + - - -
169E PHE* 3.3 25.8 - - - +
181E SER* 4.3 8.1 + - - -
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Residues in contact with SER 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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132D VAL* 4.2 0.3 - - - +
133D CYS* 2.8 40.2 + - - -
135D LEU* 4.8 0.6 - - - +
145D VAL* 4.0 16.8 - - - +
147D TRP* 3.1 30.2 + - - -
158D VAL* 3.4 5.2 - - - +
159D LEU 3.5 0.2 - - - -
160D ASN* 2.5 24.6 + - - -
174D MET* 3.8 9.4 - - - -
175D SER* 1.3 73.2 - - - +
177D THR* 1.3 63.6 + - - +
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Residues in contact with THR 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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130D SER* 4.2 12.6 - - - +
131D VAL 3.5 7.9 - - - +
132D VAL* 4.0 22.4 - - + +
157D GLY 3.4 2.9 - - - +
158D VAL* 3.3 5.3 - - - -
159D LEU* 2.8 46.1 + - + +
175D SER* 4.3 8.5 + - - -
176D SER* 1.3 78.9 + - - +
178D LEU* 1.3 60.2 + - - +
179D THR* 3.6 18.2 + - - +
144E LEU* 5.1 8.6 - - + +
179E THR* 6.0 3.4 - - + -
181E SER* 4.8 4.9 + - - -
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Residues in contact with LEU 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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129D ALA 3.7 1.6 - - - +
130D SER* 3.3 1.4 - - - -
131D VAL* 2.7 47.6 + - + +
147D TRP* 3.9 43.0 - - + +
149D ILE* 4.2 26.2 - - + -
154D ARG* 4.1 7.2 - - + -
156D ASN 3.6 23.1 - - - +
157D GLY 3.5 6.7 - - - +
158D VAL* 3.7 11.2 - - + -
177D THR* 1.3 70.6 - - - +
179D THR* 1.3 58.7 + - - +
180D LEU* 3.8 28.3 - - + -
191D TYR* 4.8 5.6 - - + -
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Residues in contact with THR 179 (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 ALA 3.8 3.6 - - - +
130D SER* 3.6 21.0 + - - +
157D GLY* 2.8 28.6 + - - +
159D LEU* 5.6 3.1 - - - +
177D THR* 3.8 13.5 + - - +
178D LEU* 1.3 72.0 - - - +
180D LEU* 1.3 75.0 + - - +
184D GLU* 5.1 0.2 - - - +
146E LYS* 4.0 17.5 + - - +
174E GLN* 3.8 25.8 + - - +
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Residues in contact with LEU 180 (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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128D GLY* 3.9 2.4 - - - -
129D ALA* 2.8 37.3 + - + +
131D VAL* 4.8 2.9 - - + -
149D ILE* 4.5 5.2 - - + -
154D ARG* 3.3 37.9 - - - +
156D ASN 5.2 0.2 - - - +
178D LEU* 3.8 26.5 - - + -
179D THR* 1.3 86.1 - - - +
181D THR* 1.3 69.0 + - - +
184D GLU* 3.4 12.8 - - + +
185D TYR* 4.1 16.4 - - + +
191D TYR* 4.0 33.4 - - + +
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Residues in contact with THR 181 (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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127D GLY 3.7 9.4 + - - -
128D GLY* 4.8 0.4 - - - -
129D ALA* 4.3 1.3 - - - -
180D LEU* 1.3 77.6 - - - +
182D LYS* 1.3 68.7 + - - +
183D ASP* 3.2 13.3 + - + +
184D GLU* 3.2 41.9 + - + +
185D TYR* 3.1 18.5 + - - +
187D ARG* 5.6 0.2 - - - +
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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