Contacts of the helix formed by residues 137 - 145 (chain W) in PDB entry 1MVW
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 GLN 137 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11W ASP* 4.2 6.7 - - - +
12W ASN 4.1 13.0 + - - +
74W GLY* 5.0 5.1 + - - -
106W THR* 3.8 23.6 + - - +
107W GLU* 3.0 35.7 + - - +
108W ALA* 3.4 11.6 - - - +
109W PRO* 4.8 7.2 - - + +
135W ALA 4.6 0.4 - - - -
136W ILE* 1.3 72.0 - - - +
138W ALA* 1.3 59.0 + - - +
140W LEU* 2.9 24.0 + - - +
141W SER* 3.1 11.3 + - - -
154W ASP* 4.0 15.9 - - - +
339W VAL* 4.0 22.0 - - + +
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Residues in contact with ALA 138 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109W PRO* 5.0 2.9 - - + +
136W ILE* 3.6 3.3 - - + +
137W GLN* 1.3 75.5 - - - +
139W VAL* 1.3 62.5 + - + +
141W SER* 3.2 3.3 + - - -
142W LEU* 2.9 21.3 + - - +
152W VAL* 3.3 33.2 - - + +
154W ASP* 4.1 8.5 + - + +
163W VAL* 3.4 44.2 - - + -
165W ILE* 3.7 2.9 - - + -
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Residues in contact with VAL 139 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135W ALA* 6.1 0.7 - - + -
136W ILE* 3.3 39.3 - - + +
137W GLN 3.0 0.6 + - - -
138W ALA* 1.3 78.3 - - + +
140W LEU* 1.3 63.3 + - + +
142W LEU* 3.5 3.3 + - - +
143W TYR* 3.3 23.9 + - + +
165W ILE* 3.5 26.9 - - + -
168W GLY* 4.2 20.0 - - - +
170W ALA* 3.9 15.9 - - + -
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Residues in contact with LEU 140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W VAL* 6.0 0.2 - - + -
104W LEU* 4.4 0.9 - - + -
106W THR* 3.4 33.2 - - + -
135W ALA* 3.6 23.8 - - + -
136W ILE 3.2 12.2 + - - +
137W GLN 2.9 5.8 + - - +
139W VAL* 1.3 76.5 - - + +
141W SER* 1.3 66.2 + - - +
143W TYR* 3.9 5.8 - - + +
144W ALA* 3.1 24.8 + - - +
338W SER 4.3 0.9 - - - -
339W VAL* 3.3 27.6 - - + +
342W GLY* 3.4 6.7 - - - +
343W GLY* 3.8 20.9 - - - +
346W LEU* 3.7 24.0 - - + -
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Residues in contact with SER 141 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637J LYS* 2.0 43.8 + - - +
137W GLN 3.1 7.6 + - - -
138W ALA* 3.2 11.9 + - - -
140W LEU* 1.3 76.9 - - - +
142W LEU* 1.3 49.9 - - - +
152W VAL* 4.3 6.1 - - - -
298W VAL* 4.6 2.5 - - - -
300W SER* 3.0 31.7 + - - -
338W SER* 3.2 11.6 - - - -
339W VAL* 3.1 27.7 + - - +
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Residues in contact with LEU 142 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637J LYS* 3.1 5.9 + - - +
138W ALA 2.9 16.9 + - - +
139W VAL* 3.8 5.2 - - - +
140W LEU 3.3 0.2 - - - -
141W SER* 1.3 74.3 - - - +
143W TYR* 1.3 60.0 + - - +
145W SER* 2.9 23.6 + - - -
147W ARG* 3.4 27.0 + - + +
148W THR* 3.6 33.0 - - - +
149W THR 3.8 2.7 - - - +
150W GLY* 3.8 25.4 - - - +
152W VAL* 3.8 16.3 - - + +
165W ILE* 3.9 20.6 - - + -
298W VAL* 3.7 26.0 - - + -
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Residues in contact with TYR 143 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541J MET* 1.9 55.4 - - - +
542J PHE* 2.3 68.1 + + + -
543J PRO* 2.1 47.3 - - + +
637J LYS* 3.7 0.3 - - - +
139W VAL* 3.3 17.5 - - + +
140W LEU* 3.9 5.8 - - + +
142W LEU* 1.3 78.8 - - - +
144W ALA* 1.3 55.3 + - - +
145W SER 3.0 0.2 - - - -
147W ARG 3.4 10.8 - - - +
148W THR* 6.0 0.2 - - + -
342W GLY* 3.7 15.5 - - - -
345W ILE* 3.5 14.1 - - + -
346W LEU* 3.8 22.9 - - + -
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Residues in contact with ALA 144 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543J PRO* 4.8 0.3 - - - +
636J LYS* 2.8 10.5 - - - +
637J LYS* 0.7 237.1 + - + +
140W LEU 3.1 17.7 + - - +
141W SER 3.4 1.8 - - - +
143W TYR* 1.3 73.2 - - - +
145W SER* 1.3 29.2 + - - -
146W GLY 3.2 2.3 + - - -
338W SER* 3.5 12.8 - - - +
342W GLY* 3.5 14.1 - - - +
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Residues in contact with SER 145 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408J VAL* 6.3 0.2 - - - -
543J PRO* 3.7 0.2 - - - -
544J LYS* 5.2 0.7 - - - +
636J LYS* 5.0 5.4 - - - -
637J LYS* 1.2 91.9 + - - +
142W LEU 2.9 5.0 + - - -
144W ALA* 1.3 46.4 - - - +
146W GLY* 1.3 55.1 + - - +
147W ARG* 3.0 45.1 + - - -
298W VAL* 3.5 14.8 - - - +
330W ILE* 5.0 2.2 - - - -
332W PRO* 4.7 13.2 - - - -
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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