Contacts of the helix formed by residues 3144 - 3157 (chain 2) in PDB entry 1BMV
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 THR3144 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10651 TRP* 4.2 13.2 - - + +
11341 MET* 2.7 62.0 - - + +
11371 SER* 3.8 3.9 + - - -
11391 TRP* 4.1 12.5 - - - +
30942 SER* 3.9 11.2 - - - +
30952 SER* 3.1 13.5 + - - -
31402 PHE* 2.9 37.2 + - + -
31412 LEU 4.9 0.2 - - - -
31422 LYS 3.2 0.2 + - - -
31432 ARG* 1.3 81.1 + - - +
31452 GLY* 1.3 59.7 + - - +
31462 PHE* 5.0 4.9 - - + +
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Residues in contact with GLY3145 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30462 LEU* 4.1 17.0 - - - -
30942 SER 4.0 0.4 - - - -
30952 SER* 3.4 22.2 - - - -
30962 ILE* 4.1 4.2 + - - -
31412 LEU 3.7 2.8 + - - -
31422 LYS 3.9 2.2 + - - -
31442 THR* 1.3 80.6 - - - +
31462 PHE* 1.3 70.4 + - - +
31472 HIS* 2.8 11.3 + - - +
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Residues in contact with PHE3146 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30462 LEU* 3.3 8.2 - - - +
30472 LEU* 2.6 46.7 + - + -
30922 MET* 3.7 23.1 - - + -
30932 ASN 3.5 15.3 - - - -
30942 SER* 3.6 24.2 + - - -
31102 GLN* 3.8 15.5 - - - -
31112 ASP* 6.0 0.2 - - - -
31272 PHE* 3.8 15.5 - + - -
31282 ASN 5.2 0.2 - - - -
31292 PRO* 3.2 44.9 - - + -
31402 PHE* 5.4 4.3 - + - -
31412 LEU* 3.2 41.4 + - + +
31442 THR* 3.8 4.1 - - + -
31452 GLY* 1.3 74.4 - - - +
31472 HIS* 1.3 61.4 - - - +
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Residues in contact with HIS3147 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11771 LEU* 4.4 4.5 - - + +
30442 SER* 3.3 14.5 - - - -
30452 ASP* 2.7 29.2 + - - -
30462 LEU* 4.6 7.2 - - + -
30472 LEU 4.5 0.7 - - - -
30912 ALA 4.2 1.6 - - - +
30922 MET* 3.3 12.7 - - - +
30932 ASN* 3.2 40.5 + - + +
30952 SER 5.1 2.0 - - - +
30962 ILE* 3.8 45.7 - - + +
31452 GLY* 2.8 9.8 + - - +
31462 PHE* 1.3 77.2 - - - +
31482 CYS* 1.3 59.5 + - - +
31492 ASP* 2.4 33.3 + - - +
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Residues in contact with CYS3148 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30432 ARG 3.7 0.5 - - - +
30442 SER* 3.7 1.4 - - - -
30452 ASP 3.4 22.9 + - - -
30472 LEU* 4.1 3.3 - - + +
30502 PHE* 3.4 32.4 - - + -
30902 CYS* 3.5 22.2 - - - -
30912 ALA 3.3 4.3 - - - -
30922 MET* 2.9 42.8 - - + -
31462 PHE 4.3 0.2 + - - -
31472 HIS* 1.3 76.8 - - - +
31492 ASP* 1.3 67.6 + - - +
31502 ILE* 4.1 6.5 - - - -
31702 TRP* 4.3 4.5 - - - -
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Residues in contact with ASP3149 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11771 LEU* 4.8 11.5 - - + +
30412 ILE* 4.4 1.7 - - + +
30432 ARG 3.8 2.2 - - - -
30442 SER* 2.5 24.0 + - - -
30892 ALA 3.5 1.7 - - - +
30902 CYS* 3.4 3.6 - - - -
30912 ALA* 2.8 41.6 + - + +
30962 ILE* 6.0 0.3 - - - +
31022 SER* 3.6 26.7 + - - -
31072 ILE* 4.0 19.7 - - + +
31472 HIS* 2.4 36.9 + - - +
31482 CYS* 1.3 73.2 - - - +
31502 ILE* 1.3 61.9 + - - +
31512 ILE* 3.9 5.0 + - + +
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Residues in contact with ILE3150 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30302 ILE* 2.9 49.6 - - + -
30412 ILE* 3.8 1.4 - - - +
30422 LEU* 2.8 40.6 + - + +
30432 ARG* 3.0 21.2 + - + +
30502 PHE* 3.0 36.3 - - + -
30882 LEU* 4.8 11.9 - - + -
30892 ALA 3.2 10.5 - - - +
30902 CYS* 4.1 17.9 - - - -
31152 TRP* 5.5 5.6 - - + -
31482 CYS* 4.3 4.0 - - - -
31492 ASP* 1.3 76.0 - - - +
31512 ILE* 1.3 55.5 + - - +
31662 VAL* 6.1 1.3 - - + -
31682 ILE* 4.6 5.8 - - + -
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Residues in contact with ILE3151 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30392 GLY* 5.5 5.4 - - - -
30402 THR 3.3 14.4 - - - +
30412 ILE* 4.9 9.0 - - + -
30422 LEU* 4.4 3.4 - - - +
30872 ALA 4.0 0.2 - - - +
30882 LEU* 3.3 5.7 - - - +
30892 ALA* 2.9 36.3 + - + -
31022 SER* 4.5 9.2 - - - +
31032 ASP 2.8 29.8 - - - +
31042 ILE* 4.0 14.6 - - + -
31072 ILE* 3.4 29.4 - - + -
31492 ASP* 4.3 6.7 - - + +
31502 ILE* 1.3 82.8 - - - +
31522 CYS* 1.3 63.8 + - - +
31532 VAL* 4.0 17.0 - - + -
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Residues in contact with CYS3152 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30322 LEU* 5.4 0.2 - - + -
30362 THR* 3.6 15.5 - - + -
30382 GLY* 3.2 27.4 - - - +
30392 GLY* 2.5 35.7 + - - +
30402 THR* 3.0 8.9 + - - +
30422 LEU* 3.9 19.0 - - + +
30862 ILE* 3.8 13.2 - - + -
30872 ALA 3.4 5.8 - - - -
30882 LEU* 4.5 3.4 - - + +
31512 ILE* 1.3 73.9 - - - +
31532 VAL* 1.3 58.5 + - - +
31542 THR 3.9 0.9 - - - -
31552 GLY* 3.5 26.0 - - - -
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Residues in contact with VAL3153 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20142 TRP* 4.3 9.2 - - + +
20172 LYS* 3.2 21.2 + - + -
20712 MET* 3.7 24.2 - - + -
21902 ILE 5.3 0.3 - - - +
21922 GLN 4.6 0.2 - - - -
30382 GLY* 4.5 6.2 - - - -
30392 GLY* 4.6 1.5 + - - +
30872 ALA 2.6 19.4 + - - +
30892 ALA* 4.3 5.8 - - + -
31042 ILE* 3.9 26.9 - - + -
31142 LEU* 3.3 26.7 - - + -
31512 ILE* 4.0 19.3 - - + +
31522 CYS* 1.3 76.1 - - - +
31542 THR* 1.3 64.1 + - - +
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Residues in contact with THR3154 (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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20172 LYS* 2.8 28.0 + - - -
20712 MET* 2.9 50.9 - - + +
20722 THR* 4.8 0.7 - - - +
21612 VAL* 3.5 15.3 - - + +
21922 GLN* 2.6 23.2 + - + +
30862 ILE* 3.7 1.2 - - - -
30872 ALA 3.1 20.2 + - - -
31522 CYS* 3.9 2.2 - - - -
31532 VAL* 1.3 78.0 - - - +
31552 GLY* 1.3 67.0 - - - +
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Residues in contact with GLY3155 (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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21922 GLN* 2.7 30.8 + - - +
30362 THR 4.3 2.7 - - - -
30372 VAL 3.9 9.9 - - - -
30382 GLY* 3.9 1.8 - - - -
30852 GLY 3.4 5.7 - - - +
30862 ILE* 3.7 3.4 - - - -
31522 CYS* 3.5 22.0 - - - -
31542 THR* 1.3 85.0 - - - +
31562 TRP* 1.4 66.0 + - - +
31572 THR* 3.8 1.7 + - - -
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Residues in contact with TRP3156 (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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21922 GLN* 4.0 13.7 - - - +
30322 LEU* 4.2 26.7 - - + +
30332 PRO 3.9 6.3 + - - -
30342 LYS* 3.7 25.5 - - - +
30362 THR* 3.8 24.6 + - - +
30782 VAL* 6.0 1.1 - - + -
30802 ILE* 3.3 37.9 - - + -
30842 THR* 3.8 7.2 - - + -
30852 GLY 3.3 8.5 - - - -
30862 ILE* 3.3 34.2 - - + +
31552 GLY* 1.4 73.4 - - - +
31572 THR* 1.3 60.9 + - - +
31582 ALA 3.5 23.6 - - - +
31592 THR* 4.5 3.8 - - - -
31602 PRO* 3.7 28.5 - - + -
31642 VAL* 4.1 22.9 - - + -
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Residues in contact with THR3157 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20712 MET 4.7 0.2 + - - -
20722 THR* 4.0 6.0 - - - +
20732 SER* 3.5 24.8 + - - +
20762 ILE* 3.5 32.3 - - + -
21562 ILE* 4.1 10.3 - - + +
21572 PRO 3.8 16.9 - - - +
21582 GLY* 4.8 2.2 - - - -
21922 GLN* 4.6 11.9 + - - +
30842 THR* 3.5 2.1 + - - -
30852 GLY 2.9 28.4 + - - -
31552 GLY 4.4 1.4 + - - -
31562 TRP* 1.3 74.1 - - - +
31582 ALA* 1.3 60.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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