Contacts of the strand formed by residues 176 - 185 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87Y THR* 5.8 2.1 - - - +
110Y THR* 4.4 15.6 - - + +
144Y ASP* 3.1 8.7 + - - -
145Y TYR* 2.9 60.6 + - + +
146Y PHE* 3.8 25.3 - + - -
147Y PRO* 4.3 0.7 - - + -
148Y GLU* 3.7 52.5 + - + +
168Y ALA* 4.0 6.3 - - + -
169Y VAL 3.3 8.3 - - - +
170Y LEU* 3.5 44.6 - - + +
175Y LEU* 1.3 72.9 - - - +
177Y SER* 1.3 62.2 + - - +
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Residues in contact with SER 177 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178X THR* 5.9 2.1 - - - +
141Y LEU* 4.4 8.8 - - - +
142Y VAL 3.3 9.3 + - - -
143Y LYS* 3.6 17.7 - - - +
144Y ASP 4.2 4.3 - - - -
145Y TYR* 3.7 2.7 - - - -
167Y PRO 4.5 0.2 - - - +
168Y ALA* 4.4 0.4 - - - -
169Y VAL* 2.9 40.9 + - - +
171Y GLN* 3.3 29.5 + - - -
176Y TYR* 1.3 77.8 - - - +
178Y LEU* 1.3 62.9 + - - +
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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
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141Y LEU* 3.8 4.8 - - - +
142Y VAL* 2.7 52.9 + - + +
145Y TYR* 2.8 31.0 - - + +
148Y GLU* 5.3 0.4 - - - +
150Y VAL* 3.8 31.6 - - + +
152Y VAL* 4.2 6.1 - - + -
165Y THR* 4.1 22.2 - - + -
166Y PHE 3.8 18.2 - - - +
167Y PRO* 4.1 2.5 - - + +
168Y ALA* 3.9 16.2 - - + +
177Y SER* 1.3 75.6 + - - +
179Y SER* 1.3 60.3 + - - +
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Residues in contact with SER 179 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133X VAL* 4.9 3.9 - - - +
176X SER* 3.1 25.2 + - - -
178X THR* 5.4 0.8 + - - -
124Y LEU* 4.4 8.7 - - - -
140Y CYS 3.3 11.7 - - - -
141Y LEU* 4.1 13.7 - - - -
165Y THR* 3.8 4.2 - - - +
166Y PHE* 3.0 45.4 + - - +
178Y LEU* 1.3 78.6 - - - +
180Y SER* 1.3 61.1 + - - +
181Y VAL* 4.3 9.0 - - - +
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Residues in contact with SER 180 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139Y GLY* 3.1 0.8 - - - -
140Y CYS* 2.8 35.9 + - - +
142Y VAL* 5.7 0.8 - - - +
152Y VAL* 3.7 25.1 - - - +
154Y TRP* 3.0 26.6 + - - -
163Y VAL* 3.9 3.1 - - - +
164Y HIS 3.5 4.7 + - - -
165Y THR* 3.0 27.2 + - - +
178Y LEU* 4.9 0.8 - - - +
179Y SER* 1.3 72.4 - - - +
181Y VAL* 1.3 67.2 + - - +
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Residues in contact with VAL 181 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118X PHE* 4.9 5.4 - - + -
133X VAL* 6.0 1.8 - - + -
135X LEU* 3.0 39.3 - - + -
137X ASN* 5.4 2.2 - - - +
176X SER* 5.8 0.2 - - - -
124Y LEU* 4.5 11.9 - - + -
137Y ALA* 4.9 2.0 - - + -
138Y LEU 3.3 13.5 - - - +
139Y GLY* 4.0 0.7 - - - -
154Y TRP* 4.3 1.5 - - - +
162Y GLY 3.8 0.3 - - - +
163Y VAL* 3.4 2.6 - - - +
164Y HIS* 2.8 37.5 + - + +
166Y PHE* 3.8 22.2 - - + -
179Y SER* 4.3 10.1 - - - +
180Y SER* 1.3 89.2 + - - +
182Y VAL* 1.3 70.1 + - - +
183Y THR* 6.0 0.2 - - + -
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Residues in contact with VAL 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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136Y ALA 3.9 0.2 - - - +
137Y ALA* 3.3 3.4 - - - -
138Y LEU* 2.7 62.1 + - + +
154Y TRP* 4.2 21.1 - - + -
159Y LEU* 4.2 15.0 - - + -
161Y SER 4.2 4.5 - - - +
162Y GLY 3.3 20.4 - - - +
163Y VAL* 3.9 15.7 - - + +
181Y VAL* 1.3 78.4 - - - +
183Y THR* 1.3 78.1 + - - +
184Y VAL* 4.1 10.5 - - + -
194Y TYR* 5.3 0.2 - - + -
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Residues in contact with THR 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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116X PHE* 4.4 10.3 - - + -
135X LEU* 5.6 1.1 - - + -
137X ASN* 3.5 28.7 + - - +
138X ASN* 5.7 1.4 + - - -
135Y THR* 4.3 11.0 - - + +
136Y ALA 3.2 6.3 - - - +
137Y ALA* 3.7 21.8 - - + -
161Y SER 4.1 9.7 - - - +
162Y GLY* 3.3 15.6 + - - -
164Y HIS* 6.0 0.2 - - - -
181Y VAL* 6.0 0.2 - - + -
182Y VAL* 1.3 77.6 - - - +
184Y VAL* 1.3 69.5 + - - +
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Residues in contact with VAL 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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135Y THR* 3.1 6.5 + - - -
136Y ALA* 2.8 36.6 + - + +
138Y LEU* 4.2 11.4 - - + -
159Y LEU* 4.6 6.5 - - + -
182Y VAL* 4.1 18.6 + - + +
183Y THR* 1.3 80.6 - - - +
185Y PRO* 1.3 82.5 - - + +
188Y SER* 3.7 0.9 - - - +
189Y LEU* 4.5 6.5 - - + -
194Y TYR* 3.4 51.4 - - + +
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Residues in contact with PRO 185 (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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134Y GLY 3.8 8.1 - - - +
135Y THR* 4.3 3.1 - - - +
184Y VAL* 1.3 91.7 - - + +
186Y SER* 1.3 62.7 + - - +
187Y SER* 4.0 14.8 - - - +
188Y SER* 2.3 43.3 + - - +
189Y LEU* 4.2 1.0 + - - +
194Y 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