Contacts of the helix formed by residues 137 - 145 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112 ASP* 4.2 7.6 - - - +
122 ASN 4.1 13.5 + - - +
742 GLY* 5.0 5.5 + - - -
1062 THR* 3.8 21.7 + - - +
1072 GLU* 3.0 34.9 + - - +
1082 ALA* 3.4 10.9 - - - +
1092 PRO* 4.8 6.6 - - + +
1362 ILE* 1.3 73.0 - - - +
1382 ALA* 1.3 59.7 + - - +
1402 LEU* 2.9 23.4 + - - +
1412 SER* 3.1 11.1 + - - -
1542 ASP* 4.0 15.7 - - - +
3392 VAL* 4.0 21.4 - - + +
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Residues in contact with ALA 138 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092 PRO* 5.0 2.7 - - + +
1362 ILE* 3.6 3.9 - - + +
1372 GLN* 1.3 75.5 - - - +
1392 VAL* 1.3 62.4 + - + +
1412 SER* 3.2 3.8 + - - -
1422 LEU* 2.9 21.8 + - - +
1522 VAL* 3.3 33.0 - - + +
1542 ASP* 4.1 8.4 + - + +
1632 VAL* 3.4 44.0 - - + -
1652 ILE* 3.7 3.4 - - + -
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Residues in contact with VAL 139 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1352 ALA* 6.1 0.7 - - + -
1362 ILE* 3.3 38.8 - - + +
1372 GLN 3.0 0.2 + - - -
1382 ALA* 1.3 78.3 - - + +
1402 LEU* 1.3 62.4 + - + +
1422 LEU* 3.5 2.8 + - - +
1432 TYR* 3.3 24.3 + - + +
1652 ILE* 3.5 26.5 - - + -
1682 GLY* 4.2 20.0 - - - +
1702 ALA* 3.9 16.2 - - + +
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Residues in contact with LEU 140 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042 LEU* 4.4 0.9 - - + -
1062 THR* 3.4 33.0 - - + -
1352 ALA* 3.6 28.7 - - + -
1362 ILE 3.2 6.4 + - - +
1372 GLN* 2.9 6.2 + - - +
1392 VAL* 1.3 76.0 - - + +
1412 SER* 1.3 67.1 + - - +
1432 TYR* 4.4 5.6 - - + -
1442 ALA* 3.1 24.9 + - - +
3382 SER 4.3 1.1 - - - -
3392 VAL* 3.3 27.4 - - + +
3402 TRP* 5.7 0.2 - - - -
3422 GLY* 3.4 6.8 - - - +
3432 GLY* 3.8 21.8 - - - +
3462 LEU* 3.7 23.6 - - + -
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Residues in contact with SER 141 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372 GLN 3.1 7.7 + - - -
1382 ALA* 3.2 11.2 + - - -
1402 LEU* 1.3 80.4 - - - +
1422 LEU* 1.3 61.9 + - - +
1442 ALA* 3.3 10.9 + - - +
1452 SER* 3.4 10.9 + - - -
1522 VAL* 4.3 5.8 - - - -
2982 VAL* 4.5 6.0 - - - +
3002 SER* 3.0 30.8 + - - -
3382 SER* 3.2 14.8 + - - -
3392 VAL* 3.1 28.6 + - - +
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Residues in contact with LEU 142 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382 ALA 2.9 16.3 + - - +
1392 VAL* 3.8 5.8 - - - +
1412 SER* 1.3 75.0 - - - +
1432 TYR* 1.3 59.0 + - - +
1452 SER* 2.9 25.6 + - - -
1472 ARG* 3.4 27.4 + - + +
1482 THR* 3.6 33.9 - - - +
1492 THR 3.8 2.5 - - - +
1502 GLY* 3.8 24.2 - - - +
1522 VAL* 3.8 16.3 - - + +
1652 ILE* 3.9 21.1 - - + -
2982 VAL* 3.7 29.2 - - + -
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Residues in contact with TYR 143 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392 VAL* 3.3 17.9 + - + +
1402 LEU* 3.9 5.8 - - + +
1422 LEU* 1.3 77.7 - - + +
1442 ALA* 1.3 59.1 + - - +
1452 SER 3.0 1.8 - - - -
1462 GLY* 2.9 28.2 + - - -
1472 ARG 3.4 14.1 - - - +
1482 THR* 5.0 10.3 - - + -
3422 GLY* 3.7 16.2 - - - -
3452 ILE* 3.5 33.8 - - + +
3462 LEU* 3.8 29.7 - - + +
3492 LEU* 4.2 17.8 - - - +
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Residues in contact with ALA 144 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1402 LEU 3.1 19.1 + - - +
1412 SER 3.3 6.3 + - - +
1432 TYR* 1.3 77.0 - - - +
1452 SER* 1.3 56.1 + - - +
1462 GLY 3.2 3.4 + - - -
3342 GLU* 5.2 7.2 - - - +
3382 SER* 3.5 16.8 - - - +
3412 ILE* 4.3 11.4 - - + +
3422 GLY* 3.5 21.1 - - - +
3452 ILE* 4.4 12.3 - - - +
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Residues in contact with SER 145 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412 SER 3.4 8.2 + - - -
1422 LEU 2.9 12.6 + - - -
1442 ALA* 1.3 76.8 - - - +
1462 GLY* 1.3 53.4 + - - +
1472 ARG* 3.0 45.3 + - - -
2982 VAL* 3.5 21.8 - - - +
3302 ILE* 5.0 2.7 - - - -
3322 PRO* 4.7 17.9 - - - -
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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