Contacts of the helix formed by residues 137 - 145 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119 ASP* 4.2 6.3 - - - +
129 ASN 4.1 13.3 + - - +
749 GLY* 5.0 5.5 + - - -
1069 THR* 3.8 24.3 + - - +
1079 GLU* 3.0 35.2 + - - +
1089 ALA* 3.4 12.0 - - - +
1099 PRO* 4.8 7.2 - - + +
1369 ILE* 1.3 73.1 - - - +
1389 ALA* 1.3 59.1 + - - +
1409 LEU* 2.9 23.8 + - - +
1419 SER* 3.1 11.3 + - - -
1549 ASP* 4.0 17.1 - - - +
3399 VAL* 4.0 20.8 - - + +
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Residues in contact with ALA 138 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099 PRO* 5.0 2.7 - - + +
1369 ILE* 3.6 3.3 - - + +
1379 GLN* 1.3 76.0 - - - +
1399 VAL* 1.3 57.7 + - + +
1419 SER* 3.2 3.2 + - - -
1429 LEU* 2.9 26.3 + - - +
1529 VAL* 3.3 34.1 - - + +
1549 ASP* 4.1 9.1 + - + +
1639 VAL* 3.4 43.5 - - + -
1659 ILE* 3.7 3.1 - - + -
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Residues in contact with VAL 139 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1359 ALA* 6.1 1.1 - - + -
1369 ILE* 3.3 39.3 - - + +
1379 GLN 3.1 0.2 - - - -
1389 ALA* 1.3 78.3 - - - +
1409 LEU* 1.3 60.9 + - + +
1429 LEU* 3.5 2.9 + - - +
1439 TYR* 3.3 24.7 + - + +
1659 ILE* 3.5 26.5 - - + -
1689 GLY* 4.2 19.7 - - - +
1709 ALA* 3.9 15.9 - - + +
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Residues in contact with LEU 140 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049 LEU* 4.4 1.6 - - + -
1069 THR* 3.4 32.8 - - + -
1359 ALA* 3.6 30.1 - - + -
1369 ILE 3.2 6.8 + - - +
1379 GLN 2.9 6.4 + - - +
1399 VAL* 1.3 75.6 - - + +
1419 SER* 1.3 66.9 + - - +
1439 TYR* 4.4 5.4 - - + -
1449 ALA* 3.1 24.8 + - - +
3389 SER 4.3 0.7 - - - -
3399 VAL* 3.3 26.7 - - + +
3409 TRP* 5.7 0.2 - - - -
3429 GLY* 3.4 7.6 - - - +
3439 GLY* 3.8 21.1 - - - +
3469 LEU* 3.7 23.6 - - + -
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Residues in contact with SER 141 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379 GLN 3.1 6.7 + - - -
1389 ALA* 3.2 11.0 + - - -
1409 LEU* 1.3 77.9 - - - +
1429 LEU* 1.3 49.9 - - - +
1449 ALA* 3.4 0.2 - - - +
1529 VAL* 4.3 6.1 - - - -
2989 VAL* 4.6 2.2 - - - -
3009 SER* 3.0 32.4 + - - -
3389 SER* 3.2 11.3 - - - -
3399 VAL* 3.1 28.2 + - - +
637D LYS* 2.0 44.2 + - - +
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Residues in contact with LEU 142 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1389 ALA 2.9 16.1 + - - +
1399 VAL* 3.8 5.2 - - - +
1419 SER* 1.3 75.2 - - - +
1439 TYR* 1.3 60.2 + - + +
1459 SER* 2.9 23.7 + - - -
1479 ARG* 3.4 27.6 + - + +
1489 THR* 3.6 33.2 - - - +
1499 THR 3.8 2.9 - - - +
1509 GLY* 3.8 24.2 - - - +
1529 VAL* 3.8 16.0 - - + +
1659 ILE* 3.9 21.8 - - + -
2989 VAL* 3.7 26.5 - - + -
637D LYS* 3.1 6.0 + - - +
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Residues in contact with TYR 143 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1399 VAL* 3.3 17.2 + - + +
1409 LEU* 3.9 6.5 - - + +
1429 LEU* 1.3 79.1 - - + +
1449 ALA* 1.3 54.0 + - - +
1459 SER 3.0 0.2 - - - -
1479 ARG 3.4 9.6 - - - +
1489 THR* 6.0 0.2 - - + -
3429 GLY* 3.7 15.9 - - - -
3459 ILE* 3.5 14.1 - - + -
3469 LEU* 3.8 22.0 - - + -
541D MET* 1.9 55.7 - - - +
542D PHE* 2.3 69.8 + + + -
543D PRO* 2.1 47.9 - - + +
637D LYS* 3.7 0.3 - - - +
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Residues in contact with ALA 144 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409 LEU 3.1 17.9 + - - +
1419 SER 3.4 1.8 - - - +
1439 TYR* 1.3 74.4 - - - +
1459 SER* 1.3 28.7 + - - -
1469 GLY 3.2 2.0 + - - -
3389 SER* 3.5 12.8 - - - +
3429 GLY* 3.5 13.5 - - - +
543D PRO* 4.8 0.2 - - - +
636D LYS* 2.8 11.1 - - - +
637D LYS* 0.7 237.0 + - + +
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Residues in contact with SER 145 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429 LEU 2.9 5.5 + - - -
1449 ALA* 1.3 46.2 - - - +
1469 GLY* 1.3 54.5 + - - +
1479 ARG* 3.0 44.8 + - - -
2989 VAL* 3.5 14.4 - - - +
3309 ILE* 5.0 2.0 - - - -
3329 PRO* 4.7 13.7 - - - -
408D VAL* 6.2 0.2 - - - -
543D PRO* 3.7 0.2 - - - -
544D LYS* 5.2 0.7 - - - +
636D LYS* 5.0 4.7 - - - -
637D LYS* 1.2 92.8 + - - +
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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