Contacts of the helix formed by residues 137 - 145 (chain 3) 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 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113 ASP* 4.2 6.3 - - - +
123 ASN 4.1 13.2 + - - +
743 GLY* 5.0 5.5 + - - -
1063 THR* 3.8 23.5 + - - +
1073 GLU* 3.0 33.6 + - - +
1083 ALA* 3.4 11.2 - - - +
1093 PRO* 4.8 7.2 - - + +
1353 ALA 4.6 0.2 - - - -
1363 ILE* 1.3 72.4 - - - +
1383 ALA* 1.3 58.3 + - - +
1403 LEU* 2.9 24.0 + - - +
1413 SER* 3.1 11.8 + - - -
1543 ASP* 4.0 16.1 - - - +
3393 VAL* 4.0 21.3 - - + +
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Residues in contact with ALA 138 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093 PRO* 5.0 3.3 - - + +
1363 ILE* 3.6 3.5 - - + +
1373 GLN* 1.3 75.5 - - - +
1393 VAL* 1.3 62.4 + - + +
1413 SER* 3.2 3.0 + - - -
1423 LEU* 2.9 21.0 + - - +
1523 VAL* 3.3 32.7 - - + +
1543 ASP* 4.1 9.1 + - + +
1633 VAL* 3.4 44.4 - - + -
1653 ILE* 3.7 3.4 - - + -
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Residues in contact with VAL 139 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1353 ALA* 6.1 0.9 - - + -
1363 ILE* 3.3 38.4 - - + +
1373 GLN 3.0 0.4 + - - -
1383 ALA* 1.3 78.1 - - - +
1403 LEU* 1.3 63.1 + - + +
1423 LEU* 3.5 3.0 + - - +
1433 TYR* 3.3 23.7 + - + +
1653 ILE* 3.5 27.1 - - + -
1683 GLY* 4.2 19.1 - - - +
1703 ALA* 3.9 15.7 - - + -
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Residues in contact with LEU 140 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043 LEU* 4.4 0.7 - - + -
1063 THR* 3.4 33.7 - - + -
1353 ALA* 3.6 28.3 - - + -
1363 ILE 3.2 8.4 + - - +
1373 GLN 2.9 6.8 + - - +
1393 VAL* 1.3 75.4 - - + +
1413 SER* 1.3 67.0 + - - +
1433 TYR* 4.4 5.8 - - + -
1443 ALA* 3.1 24.9 + - - +
3383 SER 4.3 0.9 - - - -
3393 VAL* 3.3 27.1 - - + +
3423 GLY* 3.4 7.0 - - - +
3433 GLY* 3.8 22.2 - - - +
3463 LEU* 3.7 23.8 - - + -
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Residues in contact with SER 141 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373 GLN 3.1 7.4 + - - -
1383 ALA* 3.2 12.1 + - - -
1403 LEU* 1.3 80.8 - - - +
1423 LEU* 1.3 62.3 + - - +
1443 ALA* 3.3 10.2 + - - +
1453 SER* 3.4 11.1 + - - -
1523 VAL* 4.3 6.1 - - - -
2983 VAL* 4.5 6.0 - - - +
3003 SER* 3.0 31.4 + - - -
3383 SER* 3.2 14.8 + - - -
3393 VAL* 3.1 27.7 + - - +
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Residues in contact with LEU 142 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1383 ALA 2.9 16.5 + - - +
1393 VAL* 3.8 5.4 - - - +
1413 SER* 1.3 76.7 - - - +
1433 TYR* 1.3 59.2 - - - +
1453 SER* 2.9 25.6 + - - -
1473 ARG* 3.4 27.2 + - + +
1483 THR* 3.6 33.2 - - - +
1493 THR 3.8 3.1 - - - +
1503 GLY* 3.8 24.2 - - - +
1523 VAL* 3.8 16.3 - - + +
1653 ILE* 3.9 20.4 - - + -
2983 VAL* 3.7 29.4 - - + -
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Residues in contact with TYR 143 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1393 VAL* 3.3 16.8 - - + +
1403 LEU* 3.9 5.8 - - + +
1423 LEU* 1.3 79.0 - - - +
1443 ALA* 1.3 59.9 + - - +
1453 SER 3.0 0.4 - - - -
1463 GLY* 2.9 27.8 + - - +
1473 ARG 3.4 13.9 - - - +
1483 THR* 5.0 11.4 - - + -
3423 GLY* 3.7 15.3 - - - -
3453 ILE* 3.5 33.6 - - + +
3463 LEU* 3.8 29.8 - - + +
3493 LEU* 4.2 17.2 - - - +
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Residues in contact with ALA 144 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403 LEU 3.1 18.4 + - - +
1413 SER 3.4 6.5 - - - +
1433 TYR* 1.3 77.0 - - - +
1453 SER* 1.3 56.1 + - - +
1463 GLY 3.2 3.0 + - - -
3343 GLU* 5.2 7.4 - - - +
3383 SER* 3.5 16.8 - - - +
3413 ILE* 4.3 11.0 - - + +
3423 GLY* 3.5 21.8 - - - +
3453 ILE* 4.4 13.0 - - - +
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Residues in contact with SER 145 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413 SER 3.4 8.6 + - - -
1423 LEU 2.9 11.9 + - - -
1443 ALA* 1.3 73.1 - - - +
1463 GLY* 1.3 54.8 + - - +
1473 ARG* 3.0 45.0 + - - -
2983 VAL* 3.5 22.3 - - - +
3303 ILE* 4.9 2.9 - - - +
3323 PRO* 4.7 17.0 - - - -
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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