Contacts of the strand formed by residues 176 - 185 (chain F) in PDB entry 4MXV
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 176 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ASP* 3.1 22.3 + - - -
145F TYR* 2.8 46.4 + - + +
146F PHE* 3.9 25.6 - + - -
147F PRO* 4.6 0.7 - - + -
148F GLU* 3.6 51.0 + - + +
168F ALA* 4.1 6.5 - - + -
169F VAL* 3.2 21.3 - - - -
170F LEU* 3.5 36.0 - - + +
171F GLN* 4.4 0.2 - - - -
175F LEU* 1.3 74.8 - - - +
177F SER* 1.3 63.1 + - - +
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Residues in contact with SER 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E THR* 5.8 3.1 - - - +
141F LEU* 4.0 10.2 - - - +
142F VAL 3.1 14.6 + - - -
143F LYS* 3.8 16.6 - - - +
145F TYR* 3.7 3.1 - - - -
167F PRO 4.8 0.5 - - - +
168F ALA* 3.7 0.6 - - - -
169F VAL* 3.1 33.8 + - - +
171F GLN* 3.1 27.9 + - - -
176F TYR* 1.3 80.1 - - - +
178F LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F LEU* 3.4 6.8 - - - +
142F VAL* 2.6 54.1 + - + +
145F TYR* 3.2 22.3 - - - +
150F VAL* 4.1 19.1 - - + +
152F VAL* 3.7 29.6 - - + -
165F THR* 4.0 15.0 - - + -
166F PHE 3.9 20.4 - - - +
167F PRO 4.4 2.2 - - - +
168F ALA* 3.9 15.3 - - + +
177F SER* 1.3 75.0 - - - +
179F SER* 1.3 61.2 + - - +
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Residues in contact with SER 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E VAL* 4.8 5.1 - - - +
176E SER* 3.3 27.0 + - - -
178E THR* 5.2 1.8 + - - -
124F LEU* 4.3 15.3 - - - -
140F CYS 3.1 12.1 - - - -
141F LEU* 3.9 13.2 - - - -
165F THR* 3.8 1.2 - - - +
166F PHE* 3.1 35.1 + - - +
178F LEU* 1.3 82.8 - - - +
180F SER* 1.3 61.3 + - - +
181F VAL* 5.5 1.6 - - - +
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Residues in contact with SER 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F LEU* 4.4 0.5 - - - +
139F GLY* 3.0 3.6 - - - -
140F CYS* 2.8 33.6 + - - +
142F VAL* 6.1 0.2 - - - -
152F VAL* 3.5 28.7 - - - +
154F TRP* 2.8 29.8 + - - -
163F VAL* 3.9 1.2 - - - +
164F HIS 3.5 4.5 - - - -
165F THR* 2.9 23.0 + - - +
178F LEU* 4.6 0.8 - - - +
179F SER* 1.3 73.4 - - - +
181F VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E PHE* 4.6 6.7 - - + -
133E VAL* 6.2 1.1 - - + -
135E LEU* 3.6 43.3 - - + -
137E ASN* 5.0 3.1 - - - +
124F LEU* 4.2 15.0 - - + -
138F LEU 3.2 15.7 - - - +
139F GLY* 3.9 4.9 - - - -
154F TRP* 4.3 2.2 - - - +
162F GLY 5.4 0.2 - - - +
163F VAL* 3.3 5.5 - - - +
164F HIS* 2.8 45.4 + - + +
166F PHE* 4.4 8.1 - - + -
179F SER* 5.5 2.0 - - - -
180F SER* 1.3 84.5 + - - +
182F VAL* 1.3 69.0 + - - +
183F THR* 5.6 1.6 - - + -
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Residues in contact with VAL 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ALA 3.9 0.3 - - - +
137F ALA* 3.3 2.8 - - - +
138F LEU* 2.7 63.6 + - + +
154F TRP* 4.2 13.0 - - + -
159F LEU* 4.1 20.0 - - + -
161F SER 3.9 6.7 - - - +
162F GLY 3.2 18.4 - - - +
163F VAL* 3.9 17.5 - - + -
181F VAL* 1.3 78.1 - - - +
183F THR* 1.3 76.0 + - - +
184F VAL* 4.0 11.4 + - + -
194F TYR* 5.2 0.2 - - + -
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Residues in contact with THR 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E PHE* 4.6 9.4 - - + -
135E LEU* 5.3 2.0 - - + -
137E ASN* 3.6 29.0 + - - +
138E ASN* 5.9 0.5 + - - -
135F THR* 4.2 14.6 - - + -
136F ALA 3.3 5.8 - - - +
137F ALA* 4.0 20.0 - - + -
161F SER 4.2 8.0 - - - +
162F GLY* 3.3 16.1 + - - +
181F VAL* 5.6 1.3 - - + -
182F VAL* 1.3 81.8 - - - +
184F VAL* 1.3 67.7 + - - +
185F PRO* 4.8 0.2 - - - +
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Residues in contact with VAL 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F THR* 4.0 4.0 - - - -
136F ALA* 2.8 39.8 + - - +
138F LEU* 4.8 3.8 - - + -
159F LEU* 4.9 4.7 - - + -
182F VAL* 4.0 22.4 - - + +
183F THR* 1.3 81.9 - - - +
185F PRO* 1.3 70.5 - - + +
188F SER* 3.2 17.7 - - - +
189F LEU* 4.0 13.2 - - + -
194F TYR* 3.4 43.1 - - + +
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Residues in contact with PRO 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F GLY 3.6 11.9 - - - +
135F THR* 4.3 6.0 - - + +
183F THR 4.8 0.2 - - - +
184F VAL* 1.3 89.2 - - + +
186F SER* 1.3 63.4 + - - +
187F SER* 3.8 15.7 - - - +
188F SER* 2.4 41.4 + - - +
189F LEU* 4.1 0.5 + - - +
194F TYR* 5.3 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