Contacts of the strand formed by residues 129 - 139 (chain X) 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 129 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124X GLN* 3.3 34.5 + - - +
125X LEU* 3.9 4.9 - - - +
127X SER* 3.2 16.7 + - - +
128X GLY* 1.3 82.7 - - - +
130X ALA* 1.3 62.3 + - - +
180X THR* 5.7 4.0 - - - +
181X LEU 4.2 2.0 - - - +
182X SER* 4.7 9.6 - - - +
183X LYS 4.0 3.4 - - - +
143Y LYS* 4.8 17.1 + - - +
144Y ASP* 5.6 0.9 + - - -
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Residues in contact with ALA 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X PRO* 4.0 8.3 - - + -
124X GLN* 3.8 1.6 - - - -
125X LEU* 3.8 20.6 - - + -
129X THR* 1.3 76.8 - - - +
131X SER* 1.3 62.2 + - - +
132X VAL* 4.0 1.5 + - - +
179X LEU 3.8 0.7 - - - +
180X THR* 3.5 2.4 - - - -
181X LEU* 2.9 47.5 + - + +
182X SER 4.3 1.6 - - - +
183X LYS 4.6 0.2 - - - +
186X TYR* 3.8 28.7 - - + -
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Residues in contact with SER 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X PRO 4.2 1.6 - - - +
120X PRO* 3.6 22.0 - - - +
124X GLN* 3.1 24.5 + - - +
129X THR* 5.9 0.2 - - - -
130X ALA* 1.3 72.3 - - - +
132X VAL* 1.3 61.2 + - - +
133X VAL* 4.1 3.7 + - - +
178X THR* 4.0 12.2 - - - +
179X LEU 3.4 4.7 - - - -
180X THR* 3.7 10.4 + - - -
124Y LEU* 5.9 1.4 - - - +
141Y LEU* 3.5 23.6 - - - +
143Y LYS* 3.5 22.5 - - - -
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Residues in contact with VAL 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117X ILE* 4.5 2.5 - - + -
118X PHE 3.5 13.9 - - - +
120X PRO* 4.1 19.1 - - + -
130X ALA 4.9 3.1 - - - +
131X SER* 1.3 77.0 - - - +
133X VAL* 1.3 63.2 - - - +
148X TRP* 3.6 26.3 - - + -
178X THR* 3.4 2.3 - - - -
179X LEU* 2.7 53.4 + - + +
181X LEU* 5.6 1.8 - - + -
186X TYR* 4.4 7.0 - - + -
192X TYR* 4.4 22.2 - - + -
209X PHE* 4.0 18.8 - - + -
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Residues in contact with VAL 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117X ILE* 3.6 3.3 - - - +
118X PHE* 2.8 59.4 + - + +
131X SER 4.8 1.3 - - - +
132X VAL* 1.3 78.2 - - - +
134X CYS* 1.3 71.7 + - - +
135X LEU* 4.6 1.8 - - + +
148X TRP* 3.9 2.5 - - - -
176X SER* 4.1 14.1 - - - +
177X SER 3.3 7.2 - - - +
178X THR* 3.7 23.1 - - + +
124Y LEU* 4.4 22.0 - - + -
141Y LEU* 4.4 21.1 - - + -
179Y SER* 4.9 2.7 - - - +
181Y VAL* 6.0 2.0 - - + -
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Residues in contact with CYS 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115X VAL* 4.0 10.3 - - - -
116X PHE 3.5 4.0 - - - -
117X ILE* 4.6 0.9 - - - +
133X VAL* 1.3 76.0 - - - +
135X LEU* 1.3 63.5 + - - +
136X LEU* 3.6 24.5 + - - +
146X VAL* 4.6 2.5 - - + -
148X TRP* 3.4 17.9 - - + -
175X LEU 3.8 0.7 - - - +
176X SER* 3.6 3.6 - - - -
177X SER* 2.8 39.3 + - - +
194X CYS* 2.0 45.1 - - + -
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Residues in contact with LEU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X SER 3.6 0.5 - - - +
115X VAL* 3.4 7.1 - - - +
116X PHE* 2.8 59.7 + - + +
118X PHE* 3.9 15.5 - - + -
133X VAL* 4.2 3.3 - - + -
134X CYS* 1.3 73.1 - - - +
136X LEU* 1.3 76.6 + - - +
137X ASN* 4.0 16.4 - - + +
175X LEU 3.5 2.0 - - - +
176X SER* 4.7 0.9 - - - +
137Y ALA* 4.1 9.4 - - + -
166Y PHE* 3.6 32.3 - - + -
181Y VAL* 3.0 34.3 - - + -
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Residues in contact with LEU 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X PRO* 4.2 12.8 - - + -
114X SER 3.9 3.1 - - - -
115X VAL* 4.7 1.8 - - + -
134X CYS* 3.6 20.6 - - - -
135X LEU* 1.3 75.7 - - - +
137X ASN* 1.3 58.8 + - - +
139X PHE* 3.9 13.0 - - + -
144X ALA* 3.9 25.4 - - + -
146X VAL* 3.7 20.2 - - + -
174X SER* 3.3 4.9 - - - -
175X LEU* 2.6 53.4 + - + +
196X VAL* 3.5 47.6 - - + -
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Residues in contact with ASN 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X ALA 4.4 0.2 - - - +
113X PRO* 3.6 1.4 - - - +
114X SER* 3.0 46.2 + - - +
116X PHE* 4.3 6.8 - - + -
135X LEU* 4.0 22.2 - - + +
136X LEU* 1.3 73.4 - - - +
138X ASN* 1.3 85.4 + - - +
139X PHE* 3.6 2.2 - - - -
174X SER* 3.0 16.9 + - - -
162Y GLY 5.6 0.2 + - - -
164Y HIS* 3.4 16.8 - - - -
181Y VAL* 5.4 1.7 - - - +
183Y THR* 3.5 33.1 + - - +
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Residues in contact with ASN 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X ALA* 4.1 8.5 - - - +
112X ALA 3.7 9.2 - - - +
114X SER* 6.2 0.2 - - - -
137X ASN* 1.3 88.1 - - - +
139X PHE* 1.3 57.3 + - - +
170X ASP* 3.9 14.5 + - - +
172X THR* 3.5 21.6 + - + +
173X TYR 3.1 8.7 + - - -
174X SER* 3.0 9.0 + - - -
164Y HIS* 3.0 29.3 + - - -
183Y THR* 5.7 1.2 + - - -
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Residues in contact with PHE 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X ALA* 3.2 16.6 - - - +
113X PRO* 3.5 33.7 - - + -
136X LEU* 3.9 12.8 - - + -
138X ASN* 1.3 75.7 - - - +
140X TYR* 1.3 64.3 + - - +
141X PRO 3.2 20.2 - - - -
142X ARG* 3.3 29.8 - - - -
144X ALA* 3.8 12.8 - - + -
163X VAL* 4.8 4.0 - - + -
172X THR* 3.4 2.9 - - - -
173X TYR* 2.9 43.9 + - + -
174X SER* 3.7 5.8 - - - -
175X LEU* 3.5 44.2 - - + -
198X HIS* 3.6 9.4 - + - +
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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