Contacts of the helix formed by residues 137 - 145 (chain 8) 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 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118 ASP* 4.2 6.4 - - - +
128 ASN 4.1 12.4 + - - +
748 GLY* 5.0 5.5 + - - -
1068 THR* 3.8 23.4 + - - +
1078 GLU* 3.0 35.0 + - - +
1088 ALA* 3.4 10.7 - - - +
1098 PRO* 4.8 7.0 - - + +
1358 ALA 4.6 0.2 - - - -
1368 ILE* 1.3 72.8 - - - +
1388 ALA* 1.3 59.3 + - - +
1408 LEU* 2.9 24.1 + - - +
1418 SER* 3.1 10.9 + - - -
1548 ASP* 4.0 15.9 - - - +
3398 VAL* 4.0 20.7 - - + +
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Residues in contact with ALA 138 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098 PRO* 5.0 2.7 - - + +
1368 ILE* 3.6 3.9 - - + +
1378 GLN* 1.3 75.9 - - - +
1398 VAL* 1.3 61.8 + - + +
1418 SER* 3.2 3.7 + - - -
1428 LEU* 2.9 22.0 + - - +
1528 VAL* 3.3 33.0 - - + +
1548 ASP* 4.1 8.4 + - + +
1638 VAL* 3.4 44.0 - - + -
1658 ILE* 3.7 3.1 - - + -
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Residues in contact with VAL 139 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1358 ALA* 6.1 0.9 - - + -
1368 ILE* 3.3 39.0 - - + +
1378 GLN 3.0 0.4 + - - -
1388 ALA* 1.3 78.1 - - + +
1408 LEU* 1.3 62.1 + - + +
1428 LEU* 3.5 2.8 + - - +
1438 TYR* 3.3 24.5 + - + +
1658 ILE* 3.5 26.2 - - + -
1688 GLY* 4.2 20.4 - - - +
1708 ALA* 3.9 15.7 - - + +
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Residues in contact with LEU 140 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048 LEU* 4.4 1.1 - - + -
1068 THR* 3.4 32.8 - - + -
1358 ALA* 3.6 28.7 - - + -
1368 ILE 3.2 6.6 + - - +
1378 GLN* 2.9 6.2 + - - +
1398 VAL* 1.3 75.6 - - + +
1418 SER* 1.3 67.3 + - - +
1438 TYR* 4.4 5.6 - - + -
1448 ALA* 3.1 25.1 + - - +
3388 SER 3.8 0.6 - - - +
3398 VAL* 3.3 27.4 - - + +
3408 TRP* 5.7 0.2 - - - -
3428 GLY* 3.4 6.8 - - - +
3438 GLY* 3.8 21.5 - - - +
3468 LEU* 3.7 24.0 - - + -
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Residues in contact with SER 141 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378 GLN 3.1 7.2 + - - -
1388 ALA* 3.2 11.4 + - - -
1408 LEU* 1.3 76.5 - - - +
1428 LEU* 1.3 49.5 - - - +
1528 VAL* 4.3 5.8 - - - -
2988 VAL* 4.6 2.0 - - - -
3008 SER* 3.0 31.6 + - - -
3388 SER* 3.2 11.9 - - - -
3398 VAL* 3.1 28.4 + - - +
637A LYS* 2.0 44.2 + - - +
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Residues in contact with LEU 142 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388 ALA 2.9 16.1 + - - +
1398 VAL* 3.8 5.2 - - - +
1418 SER* 1.3 75.0 - - - +
1438 TYR* 1.3 59.5 - - - +
1458 SER* 2.9 23.6 + - - -
1478 ARG* 3.4 27.2 + - + +
1488 THR* 3.6 33.4 - - - +
1498 THR 3.8 2.5 - - - +
1508 GLY* 3.8 24.7 - - - +
1528 VAL* 3.8 15.8 - - + +
1658 ILE* 3.9 21.5 - - + -
2988 VAL* 3.7 25.8 - - + -
637A LYS* 3.1 5.7 + - - +
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Residues in contact with TYR 143 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1398 VAL* 3.3 17.7 + - + +
1408 LEU* 3.9 5.8 - - + +
1428 LEU* 1.3 79.2 - - + +
1448 ALA* 1.3 54.1 + - - +
1458 SER 3.0 0.2 - - - -
1478 ARG 3.4 9.6 - - - +
3428 GLY* 3.7 16.6 - - - -
3458 ILE* 3.5 13.7 - - + -
3468 LEU* 3.8 21.8 - - + -
541A MET* 1.9 55.3 - - - +
542A PHE* 2.3 68.5 + + + -
543A PRO* 2.1 47.5 - - + +
637A LYS* 3.7 0.2 - - - +
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Residues in contact with ALA 144 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1408 LEU 3.1 18.0 + - - +
1418 SER 3.4 2.0 - - - +
1438 TYR* 1.3 73.6 - - - +
1458 SER* 1.3 28.5 + - - -
1468 GLY 3.2 2.6 + - - -
3388 SER* 3.5 12.6 - - - +
3428 GLY* 3.5 13.9 - - - +
543A PRO* 4.8 0.3 - - - +
636A LYS* 2.8 11.4 - - - +
637A LYS* 0.7 236.6 + - + +
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Residues in contact with SER 145 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428 LEU 2.9 5.0 + - - -
1448 ALA* 1.3 47.6 - - - +
1468 GLY* 1.3 53.4 + - - +
1478 ARG* 3.0 45.5 + - - -
2988 VAL* 3.5 14.4 - - - +
3308 ILE* 5.0 2.7 - - - -
3328 PRO* 4.7 13.2 - - - -
543A PRO* 3.7 0.2 - - - -
544A LYS* 5.1 0.7 - - - +
636A LYS* 5.0 4.7 - - - -
637A LYS* 1.2 92.3 + - - +
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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