Contacts of the strand formed by residues 135 - 145 (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 THR 135 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116X PHE* 4.2 19.9 - - + -
134Y GLY* 1.3 75.2 - - - -
136Y ALA* 1.3 61.0 + - - +
183Y THR* 4.3 10.4 - - + -
184Y VAL 3.1 21.4 + - - -
185Y PRO* 4.3 1.9 - - - +
186Y SER* 4.0 2.9 - - - +
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Residues in contact with ALA 136 (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* 4.5 3.4 - - - -
126Y PRO* 4.4 11.2 - - + -
127Y SER* 5.3 6.5 - - - +
135Y THR* 1.3 75.8 - - - +
137Y ALA* 1.3 62.0 + - - +
138Y LEU* 5.4 0.2 - - - -
183Y THR* 3.2 5.2 - - - -
184Y VAL* 2.8 45.3 + - + +
186Y SER* 4.0 10.6 - - - +
189Y LEU* 4.1 29.2 - - + -
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Residues in contact with ALA 137 (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* 3.7 38.2 - - + -
118X PHE* 3.2 18.9 - - + -
135X LEU* 4.1 12.3 - - + -
126Y PRO* 3.7 11.7 - - - +
127Y SER 4.7 1.4 + - - +
136Y ALA* 1.3 75.5 - - - +
138Y LEU* 1.3 62.5 + - - +
181Y VAL* 4.9 0.4 - - + -
182Y VAL 3.3 6.1 - - - +
183Y THR* 3.7 19.3 - - + -
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Residues in contact with LEU 138 (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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118X PHE* 4.1 3.1 - - - -
124Y LEU* 3.4 16.6 - - - +
126Y PRO* 3.5 28.7 - - + -
136Y ALA 5.2 1.1 - - - +
137Y ALA* 1.3 74.3 - - - +
139Y GLY* 1.3 58.1 + - - +
154Y TRP* 3.9 14.1 - - + -
181Y VAL* 3.3 7.5 - - - +
182Y VAL* 2.7 42.9 + - + +
184Y VAL* 4.2 13.5 - - + -
189Y LEU* 4.1 10.3 - - + -
194Y TYR* 3.7 41.5 - - + -
211Y VAL* 3.7 17.5 - - + +
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Residues in contact with GLY 139 (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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124Y LEU* 2.7 40.7 + - - +
138Y LEU* 1.3 81.7 - - - +
140Y CYS* 1.3 56.1 + - - -
154Y TRP* 3.6 16.2 - - - -
180Y SER 3.1 13.0 - - - -
181Y VAL* 4.0 1.1 - - - -
211Y VAL* 3.2 13.3 - - - +
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Residues in contact with CYS 140 (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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121Y VAL* 3.9 17.3 - - + -
122Y PHE 3.4 6.3 - - - +
124Y LEU* 4.0 5.5 - - - +
139Y GLY* 1.3 77.2 - - - -
141Y LEU* 1.3 59.8 + - - +
142Y VAL* 3.7 8.3 + - + +
152Y VAL* 5.4 0.7 - - + -
154Y TRP* 4.0 1.1 - - + -
179Y SER* 3.3 5.4 - - - -
180Y SER* 2.8 36.5 + - - +
196Y CYS* 1.5 60.6 - - + -
198Y VAL* 5.1 0.9 - - + -
209Y LYS* 4.5 2.7 - - - -
211Y VAL* 4.1 8.1 - - - -
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Residues in contact with LEU 141 (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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124X GLN* 4.6 4.0 - - - +
131X SER* 3.5 35.0 - - - +
133X VAL* 4.4 16.8 - - + -
178X THR* 4.9 7.9 - - + +
120Y SER 3.5 2.1 - - - +
121Y VAL* 3.3 5.4 - - - -
122Y PHE* 2.7 52.6 + - + +
124Y LEU* 4.0 17.0 - - + +
140Y CYS* 1.3 70.9 - - - +
142Y VAL* 1.3 62.2 + - - +
143Y LYS* 3.7 17.9 + - + -
177Y SER* 4.4 11.7 - - - +
178Y LEU 3.8 9.6 - - - +
179Y SER* 4.1 14.1 - - - -
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Residues in contact with VAL 142 (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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119Y PRO* 3.5 30.1 - - + -
120Y SER 3.6 3.1 - - - -
121Y VAL* 4.2 5.6 - - + -
140Y CYS* 4.6 8.1 - - + +
141Y LEU* 1.3 73.6 - - - +
143Y LYS* 1.3 56.9 + - - +
145Y TYR* 3.7 13.0 - - + -
150Y VAL* 4.1 8.3 - - + -
152Y VAL* 4.3 4.7 - - + -
177Y SER* 3.3 4.6 - - - -
178Y LEU* 2.7 57.1 + - + +
180Y SER 5.7 0.4 - - - +
198Y VAL* 3.7 37.9 - - + -
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Residues in contact with LYS 143 (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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124X GLN* 4.6 5.4 - - - +
129X THR* 4.8 17.9 + - - +
131X SER* 3.5 21.3 - - - +
180X THR* 4.3 10.6 + - - -
119Y PRO* 3.4 2.6 - - - +
120Y SER* 2.9 38.0 + - - +
122Y PHE* 4.0 22.4 - - + -
141Y LEU* 4.2 16.4 - - + -
142Y VAL* 1.3 75.6 - - - +
144Y ASP* 1.3 98.6 + - - +
145Y TYR* 3.8 2.2 - - - -
171Y GLN* 3.4 20.7 + - - +
173Y SER* 5.6 0.6 + - - -
176Y TYR 4.0 0.2 - - - -
177Y SER* 3.6 13.5 - - - +
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Residues in contact with ASP 144 (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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129X THR* 5.6 1.0 + - - -
117Y LYS* 2.9 35.2 + - - +
118Y GLY 3.3 3.1 - - - +
120Y SER* 5.0 4.0 + - - +
143Y LYS* 1.3 102.3 + - + +
145Y TYR* 1.3 56.1 + - - +
171Y GLN* 2.8 24.3 - - - +
173Y SER* 4.4 2.8 + - - -
175Y LEU* 3.6 21.6 - - + +
176Y TYR 3.1 14.4 + - - -
177Y SER* 4.2 1.0 - - - -
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Residues in contact with TYR 145 (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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117Y LYS 3.2 13.9 - - - +
119Y PRO* 3.6 21.5 - - + -
142Y VAL* 3.7 23.8 - - + -
144Y ASP* 1.3 76.1 - - - +
146Y PHE* 1.3 62.2 + - - +
147Y PRO 3.7 19.5 - - - -
148Y GLU* 4.0 7.1 + - - -
149Y PRO 4.5 1.1 - - - -
150Y VAL* 3.5 34.1 + - + +
168Y ALA* 3.6 10.9 - - - +
175Y LEU* 3.8 4.7 - - - +
176Y TYR* 2.9 63.9 + - + -
177Y SER* 3.7 8.3 - - - -
178Y LEU* 2.8 31.5 - - + +
200Y HIS* 4.0 3.6 - - + -
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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