Contacts of the strand formed by residues 135 - 145 (chain H) in PDB entry 3MXW
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H THR* 3.1 9.4 + - - -
132H SER* 2.6 50.1 + - - +
133H GLY 4.1 5.8 - - - +
134H GLY* 1.3 83.5 - - - +
136H ALA* 1.3 61.7 + - - +
183H THR* 4.9 11.6 - - - +
184H VAL 3.4 14.1 - - - +
185H PRO* 5.3 1.8 - - + -
186H SER* 4.3 1.6 - - - -
116L PHE* 4.3 7.7 - - - -
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Residues in contact with ALA 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H PRO* 4.2 11.9 - - + -
127H SER 5.7 1.6 - - - +
130H SER 3.2 9.6 - - - +
131H THR* 5.1 2.7 - - - -
135H THR* 1.3 75.2 - - - +
137H ALA* 1.3 61.1 + - - +
183H THR* 3.3 3.8 - - - -
184H VAL* 2.8 43.6 + - + +
186H SER* 4.1 8.3 - - - +
189H LEU* 3.9 27.4 - - + -
116L PHE* 4.5 1.6 - - - -
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Residues in contact with ALA 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PRO* 3.4 6.6 - - - +
130H SER* 3.0 26.3 + - - -
136H ALA* 1.3 75.0 - - - +
138H LEU* 1.3 63.5 + - - +
182H VAL 3.3 8.3 - - - +
183H THR* 4.0 10.5 - - + +
116L PHE* 3.6 35.8 - - + -
118L PHE* 3.4 16.7 - - + -
135L LEU* 4.0 8.7 - - + -
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H LEU* 3.3 15.5 - - - +
126H PRO* 3.6 29.2 - - + -
137H ALA* 1.3 75.5 - - - +
139H GLY* 1.3 60.0 + - - +
154H TRP* 3.6 23.6 - - + -
181H VAL* 3.2 6.7 - - - +
182H VAL* 2.8 51.7 + - + +
184H VAL* 3.8 22.9 - - + -
189H LEU* 4.4 0.9 - - + -
194H TYR* 3.6 37.2 - - + -
211H VAL* 4.0 8.5 - - + +
118L PHE* 4.1 4.3 - - - -
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Residues in contact with GLY 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H LEU* 2.8 43.1 + - - +
138H LEU* 1.3 79.5 - - - +
140H CYS* 1.3 63.7 + - - -
154H TRP* 3.5 15.7 - - - -
180H SER 3.1 12.3 - - - -
181H VAL* 4.0 1.1 - - - -
211H VAL* 3.5 8.5 - - - +
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Residues in contact with CYS 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 4.1 12.1 - - + -
122H PHE 3.3 8.3 - - - +
124H LEU* 3.9 4.4 - - - +
139H GLY* 1.3 79.9 - - - -
141H LEU* 1.3 59.6 + - - +
142H VAL* 3.9 8.4 + - + +
152H VAL* 5.6 0.2 - - + -
154H TRP* 3.9 1.5 - - + -
179H SER* 3.4 4.0 - - - -
180H SER* 2.8 34.4 + - - +
196H CYS* 2.1 52.9 - - + -
198H VAL* 5.1 0.4 - - + -
209H LYS* 4.3 4.3 - - - -
211H VAL* 3.6 16.2 - - - -
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Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H SER 3.5 1.4 - - - +
121H VAL* 3.4 5.2 - - - +
122H PHE* 2.8 61.7 + - + +
124H LEU* 4.1 15.9 - - + +
140H CYS* 1.3 71.9 - - - +
142H VAL* 1.3 60.1 + - - +
143H LYS* 3.8 10.5 + - + -
177H SER* 3.9 14.4 - - - +
178H LEU 3.7 17.7 - - - +
179H SER* 4.5 8.7 - - - +
124L GLN* 4.4 4.0 - - - +
131L SER* 3.6 32.8 - - - +
133L VAL* 4.7 15.5 - - + -
178L THR* 4.7 11.0 - - + +
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Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 3.5 26.5 - - + -
120H SER 3.5 3.1 - - - +
121H VAL* 4.5 5.6 - - + -
140H CYS* 4.4 8.3 - - + +
141H LEU* 1.3 74.5 - - - +
143H LYS* 1.3 60.0 + - - +
145H TYR* 3.7 4.7 - - + -
150H VAL* 3.9 16.6 - - + -
152H VAL* 4.3 5.8 - - + -
177H SER* 3.3 4.4 + - - -
178H LEU* 2.7 60.4 + - + +
198H VAL* 3.9 39.5 - - + -
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Residues in contact with LYS 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H PRO* 3.4 2.2 - - - +
120H SER* 2.9 42.6 + - - +
122H PHE* 4.4 15.5 - - + -
141H LEU* 4.5 10.1 - - + -
142H VAL* 1.3 73.8 - - - +
144H ASP* 1.3 102.8 + - - +
145H TYR* 3.7 1.3 - - - -
171H GLN* 3.5 15.6 + - - +
177H SER* 3.6 15.7 - - - +
124L GLN* 3.7 22.4 - - - +
129L THR* 4.5 12.1 + - - +
131L SER* 3.9 15.7 - - - +
180L THR* 4.4 15.8 - - - +
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Residues in contact with ASP 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H LYS* 2.9 35.5 + - - +
118H GLY 3.3 6.9 - - - +
120H SER* 5.4 2.4 + - - +
143H LYS* 1.3 106.7 + - - +
145H TYR* 1.3 57.5 + - - +
171H GLN* 2.7 31.1 + - - +
173H SER* 4.8 1.6 + - - -
175H LEU* 3.8 22.0 - - + +
176H TYR 2.9 14.9 + - - -
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Residues in contact with TYR 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H LYS* 3.3 13.7 - - - +
119H PRO* 3.8 24.9 - - + -
142H VAL* 3.7 22.7 - - + -
144H ASP* 1.3 77.2 - - - +
146H PHE* 1.3 62.9 + - - +
147H PRO 3.5 20.4 - - - -
148H GLU* 4.2 9.5 + - + -
150H VAL* 3.6 40.6 + - + +
168H ALA* 3.3 17.2 - - - +
175H LEU* 3.6 3.6 - - - -
176H TYR* 2.8 66.4 + + + -
177H SER* 4.0 1.8 - - - -
178H LEU* 3.2 25.9 - - + +
200H HIS* 3.7 3.8 - + + -
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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