Contacts of the strand formed by residues 177 - 185 (chain Y) in PDB entry 4MXW
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 LEU 177 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X ARG* 5.9 1.2 - - - +
195X PRO* 5.8 3.6 - - - +
196X SER* 3.9 21.3 + - - +
160Y ARG* 3.5 40.4 - - + +
161Y SER 5.3 0.2 - - - +
162Y SER* 3.1 28.0 - - - +
175Y PRO* 6.0 1.3 - - + +
176Y GLU* 1.3 79.5 - - - +
178Y LEU* 1.3 65.9 + - - +
179Y LEU 6.3 0.4 - - - -
180Y GLU* 5.1 11.9 - - + +
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Residues in contact with LEU 178 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85X ARG* 3.7 35.2 - - + +
195X PRO 3.3 22.5 - - - +
196X SER* 3.6 5.5 - - - -
135Y LEU* 4.2 8.1 - - + -
161Y SER* 3.1 13.7 + - - +
162Y SER 4.2 4.7 - - - -
163Y LEU 4.1 12.1 - - - +
176Y GLU* 3.8 19.5 - - + +
177Y LEU* 1.3 81.5 - - - +
179Y LEU* 1.3 71.0 + - + +
211Y VAL* 4.0 28.0 - - + -
213Y LEU* 4.5 1.8 - - + -
219Y VAL* 4.0 28.3 - - + -
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Residues in contact with LEU 179 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X HIS* 5.8 4.9 - - + +
195X PRO 4.8 1.1 - - - +
196X SER* 3.9 1.3 - - - -
199X PHE* 3.6 37.5 - - + -
135Y LEU* 4.0 16.4 - - + +
160Y ARG* 3.1 5.5 - - - +
161Y SER* 2.8 36.3 + - - +
177Y LEU* 6.3 0.4 - - - -
178Y LEU* 1.3 94.0 - - + +
180Y GLU* 1.3 61.8 + - - +
207Y PHE* 3.4 26.2 - - + -
208Y GLY 3.7 4.5 - - - -
209Y GLY* 3.4 40.6 - - - +
211Y VAL* 4.8 6.7 - - + -
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Residues in contact with GLU 180 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X GLN* 3.2 20.1 + - - +
114X VAL* 4.6 1.2 - - - +
196X SER* 3.1 35.9 + - - +
197X THR* 3.8 19.7 - - + +
158Y THR* 5.4 8.2 - - - +
159Y LEU 3.4 12.8 - - - +
160Y ARG* 4.1 18.6 + - + +
177Y LEU* 5.1 11.8 - - + +
179Y LEU* 1.3 76.8 - - - +
181Y GLY* 1.3 65.7 + - - +
182Y ALA* 5.6 2.0 - - + -
207Y PHE* 4.0 6.3 - - - -
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Residues in contact with GLY 181 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X GLN* 4.1 8.3 - - - -
114X VAL* 5.4 1.1 - - - -
166X SER* 3.8 7.6 - - - -
158Y THR* 3.9 0.7 - - - -
159Y LEU 2.9 30.8 + - - +
180Y GLU* 1.3 77.7 - - - +
182Y ALA* 1.3 64.1 + - - +
205Y VAL* 3.9 10.8 - - - -
207Y PHE* 3.6 17.5 - - - -
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Residues in contact with ALA 182 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X VAL* 5.2 3.3 - - + +
164X LEU* 3.7 23.3 - - + -
165X HIS* 3.6 5.8 + - - -
166X SER* 2.5 42.8 + - - +
157Y VAL 3.7 3.8 - - - -
158Y THR* 3.7 24.2 - - + +
180Y GLU* 5.6 4.3 - - + +
181Y GLY* 1.3 77.3 - - - +
183Y GLU* 1.3 63.8 + - - +
184Y THR* 6.3 0.2 - - + -
205Y VAL* 3.8 6.7 - - - +
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Residues in contact with GLU 183 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LYS* 4.7 4.9 + - - +
164X LEU* 3.7 9.6 - - - +
165X HIS* 3.3 24.6 + - - -
166X SER 5.4 3.6 + - - +
157Y VAL* 2.7 44.2 + - + +
182Y ALA* 1.3 77.6 - - - +
184Y THR* 1.3 63.4 + - - +
185Y VAL* 4.0 20.8 + - + +
203Y THR* 3.7 23.3 + - + +
204Y SER 4.4 4.3 - - - +
205Y VAL* 3.7 23.4 - - + +
183Z GLU* 3.5 15.6 - - - +
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Residues in contact with THR 184 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161X GLU* 6.4 0.9 - - - -
162X PRO 3.8 15.3 - - - +
163X TRP* 2.9 9.2 - - - +
164X LEU* 2.3 59.2 + - + +
165X HIS* 4.5 7.1 + - - -
154Y GLY* 5.4 2.5 - - - +
155Y ARG 2.9 16.6 - - - +
156Y SER* 3.3 23.3 - - - -
158Y THR* 5.9 1.3 - - + -
183Y GLU* 1.3 75.1 - - - +
185Y VAL* 1.3 63.8 + - - +
186Y THR* 5.9 1.6 - - - -
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Residues in contact with VAL 185 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165X HIS* 5.8 1.8 - - + -
155Y ARG* 2.8 37.4 + - + +
157Y VAL* 5.8 0.4 - - + +
183Y GLU* 4.0 22.9 + - + +
184Y THR* 1.3 79.4 - - - +
186Y THR* 1.3 66.0 + - - +
187Y PRO* 3.6 26.0 - - + -
201Y TRP* 5.4 9.2 - - + -
203Y THR* 5.2 13.7 - - + +
183Z GLU* 5.6 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