Contacts of the strand formed by residues 160 - 170 (chain B) in PDB entry 5I75
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 SER 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLY* 3.2 6.4 + - - -
159B SER* 1.3 87.2 + - - +
161B VAL* 1.3 64.4 - - - +
162B THR* 4.3 1.7 + - - -
207B THR* 3.9 22.1 - - - +
208B VAL 3.5 13.0 - - - -
209B PRO* 3.9 4.5 - - - -
210B SER* 3.7 2.5 - - - -
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PRO* 4.0 18.2 - - + -
157B THR* 4.0 21.3 - - + +
158B GLY 5.2 0.2 - - - +
160B SER* 1.3 74.4 - - - +
162B THR* 1.3 63.9 + - - +
163B LEU* 3.8 19.7 - - + -
207B THR* 3.8 0.4 - - - -
208B VAL* 2.9 40.3 + - + +
209B PRO 5.0 0.9 - - - +
210B SER* 3.6 23.3 - - - +
213B TRP* 4.1 28.3 - - + -
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PRO* 3.4 6.4 - - - +
160B SER* 4.3 2.1 + - - -
161B VAL* 1.3 74.7 - - - +
163B LEU* 1.3 72.1 + - - +
205B SER* 4.3 10.3 - - - -
206B VAL 3.4 7.9 - - - +
207B THR* 3.5 21.5 + - - +
134C THR* 5.6 4.7 - - - +
136C SER* 4.4 16.1 + - - +
138C PHE* 3.1 34.9 - - + -
155C PHE* 5.0 0.7 - - + -
157C ASN* 4.1 22.4 + - - +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU 4.4 2.2 - - - -
151B PRO* 3.8 16.4 - - + -
161B VAL* 3.8 15.9 - - + -
162B THR* 1.3 79.9 - - - +
164B GLY* 1.3 59.7 + - - +
179B TRP* 4.9 2.0 - - + -
205B SER* 3.1 9.5 - - - -
206B VAL* 2.9 37.7 + - + +
208B VAL* 3.9 22.2 - - + -
213B TRP* 3.7 32.3 - - + +
218B VAL* 4.2 24.9 - - + -
235B LEU* 3.6 29.4 - - + -
138C PHE* 5.0 3.6 - - - -
155C PHE* 4.9 0.3 - - - -
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 2.9 39.4 + - - +
163B LEU* 1.3 78.7 - - - +
165B CYS* 1.3 67.5 + - - -
179B TRP* 3.9 8.6 - - - -
204B SER 3.0 13.9 - - - -
205B SER* 3.8 3.6 - - - -
235B LEU* 3.6 4.1 - - - +
138C PHE* 6.1 0.2 - - - -
155C PHE* 5.0 3.6 - - - -
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Residues in contact with CYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 5.3 3.8 - - + -
147B TYR 4.1 5.8 - - - +
148B PRO* 4.5 13.2 - - - -
149B LEU* 4.1 4.9 - - - +
164B GLY* 1.3 79.3 - - - -
166B LEU* 1.3 61.4 + - - +
167B VAL* 5.4 2.0 - - - +
177B VAL* 5.2 7.6 - - + -
179B TRP* 3.8 10.8 - - + -
202B MET* 5.7 0.2 - - - +
203B SER* 3.6 2.8 - - - -
204B SER* 2.9 34.3 + - - +
220B CYS* 2.0 52.5 - - + -
222B VAL* 5.5 2.2 - - + -
233B LYS 4.5 1.6 - - - -
235B LEU* 4.9 7.0 - - - -
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B SER 3.6 0.5 - - - +
146B VAL* 3.5 5.0 - - - +
147B TYR* 2.9 51.9 + - + +
149B LEU* 3.7 23.8 - - + -
165B CYS* 1.3 74.6 - - - +
167B VAL* 1.3 71.5 + - - +
168B LYS* 4.2 7.0 - - + +
201B THR* 4.6 9.9 - - + -
202B MET 3.4 19.7 - - - +
203B SER* 4.0 11.4 - - - -
144C GLN* 4.1 22.4 - - - +
151C SER* 4.7 15.7 - - - +
153C VAL* 5.1 6.7 - - + -
198C THR* 5.6 9.6 - - + +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PRO* 3.7 28.5 - - + -
145B SER 3.5 3.4 - - - +
146B VAL* 4.8 2.2 - - + -
165B CYS 5.4 2.0 - - - +
166B LEU* 1.3 80.0 - - - +
168B LYS* 1.3 62.0 + - - +
170B TYR* 3.7 20.4 - - + -
175B VAL* 4.6 2.9 - - + -
177B VAL* 4.1 4.3 - - + -
201B THR* 3.3 5.1 - - - +
202B MET* 2.8 65.0 + - + +
222B VAL* 3.7 37.0 - - + -
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B SER* 2.9 51.7 + - - +
147B TYR* 4.8 14.0 + - + -
166B LEU* 4.2 11.4 - - + -
167B VAL* 1.3 75.7 - - - +
169B GLY* 1.3 68.0 + - - +
170B TYR* 4.7 1.6 - - - -
196B GLN* 5.9 1.3 - - - +
199B LEU* 6.4 0.9 - - - -
201B THR* 3.9 18.8 - - + +
144C GLN* 6.2 2.2 - - - +
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Residues in contact with GLY 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B THR* 3.7 7.9 - - - +
143B PRO 3.0 22.2 - - - +
144B PRO* 3.3 0.7 - - - +
145B SER* 4.8 0.7 + - - -
168B LYS* 1.3 85.9 - - - +
170B TYR* 1.3 60.3 + - - +
199B LEU* 3.9 22.4 - - - -
200B TYR 2.9 15.7 + - - -
201B THR* 3.4 2.7 + - - -
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B THR* 3.3 18.2 - - - +
144B PRO* 3.6 12.6 - - + -
167B VAL* 3.7 29.2 - - + -
169B GLY* 1.3 77.0 - - - +
171B PHE* 1.3 63.6 + - - +
172B PRO 3.2 19.7 - - - -
173B GLU* 4.3 3.4 - - - -
174B SER 4.1 4.0 - - - -
175B VAL* 3.2 33.6 - - + +
193B ALA* 3.3 25.8 - - - +
199B LEU* 3.5 4.6 - - - +
200B TYR* 2.6 68.4 + - + +
201B THR* 3.9 2.5 - - - -
202B MET* 3.6 7.3 - - + +
224B HIS* 3.2 27.6 - + - +
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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