Contacts of the strand formed by residues 172 - 180 (chain D) in PDB entry 2ESV
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 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D ASP* 6.1 0.2 - - - -
119D ASN* 3.2 42.8 - - + -
142D ASP* 4.4 6.5 - - - -
165D LEU* 5.3 0.7 - - + -
166D ASP* 4.1 0.7 + - - +
167D MET* 2.9 51.1 + - + +
168D ARG* 5.3 0.2 - - - +
170D MET* 3.3 22.6 - - + +
171D ASP* 1.3 77.3 - - - +
173D LYS* 1.3 73.3 + - - +
174D SER* 3.6 21.1 - - - -
143E LYS* 3.6 28.9 - - + +
198E ARG* 3.4 31.0 - - - -
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Residues in contact with LYS 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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13D GLU* 3.0 39.6 + - - +
81D LEU* 3.7 29.4 - - + -
115D PRO* 3.9 15.7 - - + -
116D ASP* 3.9 23.0 + - - +
117D ILE* 4.1 15.8 - - + +
118D GLN 5.4 0.9 + - - -
119D ASN 5.7 1.9 + - - +
164D VAL* 4.5 1.8 - - + -
165D LEU 3.0 12.6 - - - +
166D ASP* 4.0 17.9 - - - +
171D ASP* 4.9 10.3 + - - -
172D PHE* 1.3 92.3 - - - +
174D SER* 1.3 63.0 + - - +
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Residues in contact with SER 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 4.2 6.7 - - - +
141D THR* 4.3 3.3 + - - -
142D ASP* 3.4 25.0 + - - +
163D CYS 3.9 0.2 - - - +
164D VAL* 3.6 2.7 - - - -
165D LEU* 2.7 53.7 + - - +
172D PHE* 3.6 13.6 - - - -
173D LYS* 1.3 77.3 - - - +
175D ASN* 1.3 64.3 + - - +
176D SER* 5.7 0.9 - - - -
198E ARG* 3.2 13.2 + - - -
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Residues in contact with ASN 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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115D PRO* 4.1 6.8 - - - +
117D ILE* 3.5 11.3 - - - +
141D THR* 3.3 6.9 + - - -
142D ASP* 3.1 25.6 + - - +
143D PHE* 2.9 49.2 + - + +
144D ASP 3.7 7.7 + - - -
145D SER* 3.4 23.6 + - - +
162D LYS* 4.3 11.7 + - + +
163D CYS 3.6 4.4 - - - +
164D VAL* 3.4 25.6 - - - +
174D SER* 1.3 73.5 - - - +
176D SER* 1.3 61.2 + - - +
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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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139D LEU* 4.0 11.9 - - - -
140D PHE 3.1 11.4 - - - -
141D THR* 4.3 6.3 - - - -
143D PHE* 3.9 4.7 - - - -
162D LYS* 3.2 4.2 - - - -
163D CYS* 3.0 34.9 + - - -
165D LEU* 5.2 5.7 - - - +
174D SER* 5.2 1.7 + - - -
175D ASN* 1.3 77.4 - - - +
177D ALA* 1.3 61.0 + - - +
145E THR* 6.2 0.9 - - - -
174E CYS* 5.1 1.7 - - - +
196E ARG* 2.8 38.9 + - - +
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Residues in contact with ALA 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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139D LEU* 3.8 2.6 - - - +
140D PHE* 2.8 37.3 + - + +
143D PHE* 4.8 0.2 - - + -
149D VAL* 3.8 39.9 - - + -
159D ILE* 4.9 0.2 - - + -
160D THR* 3.6 15.5 - - - +
161D ASP 4.3 1.8 - - - +
162D LYS* 4.5 1.1 - - - -
176D SER* 1.3 74.1 - - - +
178D VAL* 1.3 64.8 + - - +
192D PHE* 3.8 10.1 - - + -
196E ARG* 4.0 1.1 - - - +
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Residues in contact with VAL 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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137D VAL* 3.6 28.9 - - + -
138D CYS 3.4 2.9 - - - +
139D LEU* 4.2 11.0 - - + -
158D TYR 3.8 0.9 - - - +
159D ILE* 3.5 3.0 - - - +
160D THR* 2.8 45.2 + - + +
177D ALA* 1.3 77.4 - - - +
179D ALA* 1.3 62.5 + - - +
180D TRP* 4.0 18.5 - - + -
192D PHE* 4.6 0.9 - - - -
147E VAL* 4.0 22.7 - - + -
149E LEU* 4.7 0.7 - - + -
194E SER* 4.2 5.2 - - - +
196E ARG* 3.9 31.4 - - - +
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Residues in contact with ALA 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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137D VAL* 3.6 1.7 - - - +
138D CYS* 2.8 41.0 + - + +
157D VAL* 5.1 0.4 - - + -
158D TYR 3.2 8.3 - - - +
159D ILE* 3.8 16.2 - - + -
178D VAL* 1.3 75.0 - - - +
180D TRP* 1.3 65.2 + - - +
186D PHE* 4.3 15.0 - - + -
191D ALA* 4.3 4.9 - - + -
192D PHE* 3.6 25.7 - - + -
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Residues in contact with TRP 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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136D SER 3.8 17.3 - - - +
137D VAL* 3.8 7.6 - - + -
157D VAL* 3.6 1.2 - - - +
158D TYR* 2.7 84.6 + + + +
160D THR* 3.9 25.6 - - + -
178D VAL* 4.0 7.9 - - + -
179D ALA* 1.3 79.3 - - - +
181D SER* 1.3 66.4 + - - +
182D ASN* 5.1 8.0 - - + +
186D PHE* 4.0 10.7 - - - -
149E LEU* 3.7 45.2 - - + +
151E THR* 4.8 4.6 - - - +
180E LEU* 3.9 13.7 - - + -
182E GLU* 6.2 0.2 - - + -
192E ALA* 3.7 31.0 - - + -
193E LEU* 5.7 0.2 - - - -
194E SER* 4.8 2.2 - - - -
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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