Contacts of the strand formed by residues 1065 - 1079 (chain 1) 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 TRP1065 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10631 ALA 3.4 0.2 - - - -
10641 ALA* 1.3 84.2 - - + +
10661 LYS* 1.3 61.7 + - - +
11291 ASN* 4.0 22.2 - - + -
11321 PHE* 3.9 27.4 - - + -
11331 GLU 3.8 11.4 - - - -
11341 MET* 3.6 39.0 - - + -
11391 TRP* 5.1 3.4 - + + -
11421 GLN* 3.8 20.6 - - - -
11721 ILE* 3.0 31.5 - - - +
11731 ALA 2.7 27.8 + - - +
30942 SER* 3.8 22.6 + - - -
31292 PRO 5.0 0.6 + - - -
31302 ASN* 4.5 4.0 - - - +
31312 PRO* 4.6 6.9 - - + +
31322 CYS* 3.4 24.8 - - - -
31402 PHE* 4.0 26.8 - + - -
31442 THR* 4.2 7.9 - - + +
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Residues in contact with LYS1066 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10351 LEU* 3.3 48.1 + - + -
10601 LEU* 3.5 22.0 + - + +
10631 ALA* 2.5 38.9 + - + +
10641 ALA* 4.4 6.5 + - - +
10651 TRP* 1.3 77.7 - - - +
10671 LYS* 1.3 59.1 + - - +
11251 VAL* 3.0 25.8 - - + +
11321 PHE* 3.8 1.0 - - - -
11331 GLU 2.8 40.9 + - - +
11351 TRP* 4.8 16.4 - - - +
11701 PHE* 4.1 23.6 - - + -
11711 GLU 3.7 2.5 - - - -
11721 ILE* 4.7 1.8 - - + +
11761 THR* 5.3 1.0 + - - -
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Residues in contact with LYS1067 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10661 LYS* 1.3 73.2 - - - +
10681 GLY* 1.3 63.0 + - - +
11251 VAL* 3.6 5.6 - - - +
11301 ASN* 4.2 19.7 + - - +
11311 GLY* 3.3 26.5 - - - +
11321 PHE* 3.7 37.2 - - + -
11691 ASN 3.5 3.6 - - - +
11701 PHE* 3.4 5.9 - - - -
11711 GLU* 2.8 61.5 + - + +
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Residues in contact with GLY1068 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10671 LYS* 1.3 80.1 - - - +
10691 CYS* 1.3 64.2 - - - -
11241 GLU* 3.3 3.5 - - - -
11251 VAL* 2.6 47.7 + - - +
11691 ASN* 3.3 21.3 - - - -
11701 PHE* 4.0 7.0 - - - -
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Residues in contact with CYS1069 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10681 GLY* 1.3 72.5 - - - -
10701 LEU* 1.3 61.6 + - - +
11221 PRO* 6.1 3.4 - - + -
11231 ILE 3.4 7.9 - - - +
11241 GLU* 3.5 31.6 - - - -
11671 SER* 2.2 49.8 + - - +
11691 ASN* 3.6 18.0 - - - +
11701 PHE* 4.0 4.5 - - - -
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Residues in contact with LEU1070 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10341 LEU 5.6 0.4 - - - +
10351 LEU* 3.7 18.4 - - + -
10561 ILE* 4.3 13.0 - - + -
10601 LEU* 3.7 20.6 - - + -
10681 GLY 4.2 0.6 + - - -
10691 CYS* 1.3 74.6 - - - +
10711 MET* 1.3 63.4 + - - +
11221 PRO* 3.8 2.4 - - - +
11231 ILE* 3.0 48.7 + - + +
11251 VAL* 4.8 2.0 - - + +
11641 LEU* 5.2 7.2 - - + -
11651 GLY 3.3 11.9 - - - +
11661 ILE* 4.1 15.0 - - + -
11671 SER 5.4 0.2 - - - -
11701 PHE* 3.0 55.9 - - + -
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Residues in contact with MET1071 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10081 TRP* 3.6 28.1 - - + -
10701 LEU* 1.3 74.7 - - - +
10721 VAL* 1.3 54.9 + - - +
11201 ILE* 4.8 7.0 - - + -
11211 PHE* 4.1 2.5 - - - +
11221 PRO* 3.7 39.0 - - + -
11641 LEU* 2.6 16.5 - - - +
11651 GLY* 2.5 46.2 + - - +
11661 ILE 5.2 1.8 - - - +
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Residues in contact with VAL1072 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10081 TRP* 4.0 1.6 - - - -
10341 LEU* 3.5 29.2 - - + -
10701 LEU* 4.2 0.4 + - + -
10711 MET* 1.3 75.5 - - - +
10731 LYS* 1.3 77.3 + - - +
10741 VAL* 3.8 15.3 - - + -
11191 LEU 4.3 0.2 - - - -
11201 ILE* 3.5 11.1 - - - +
11211 PHE* 3.0 59.5 + - + +
11231 ILE* 3.9 15.0 - - + -
11471 LEU* 4.6 5.2 - - + -
11621 VAL* 4.8 3.8 - - + -
11631 LEU 3.4 4.5 - - - +
11641 LEU* 3.7 18.4 - - + -
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Residues in contact with LYS1073 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10081 TRP* 4.1 25.1 - - + +
10721 VAL* 1.3 76.1 - - - +
10741 VAL* 1.3 63.5 + - - +
10751 VAL* 3.8 23.3 - - + +
11181 GLU* 3.4 33.6 + - + -
11191 LEU 3.5 4.0 - - - +
11201 ILE* 3.0 32.6 - - + +
11611 ASP 3.5 1.0 - - - +
11621 VAL* 3.2 4.2 - - - +
11631 LEU* 2.5 67.0 + - + +
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Residues in contact with VAL1074 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10721 VAL* 3.8 11.7 - - + -
10731 LYS* 1.3 76.4 - - - +
10751 VAL* 1.3 68.3 + - - +
11171 TRP* 3.9 16.6 - - + -
11181 GLU* 3.7 2.9 - - - +
11191 LEU* 3.3 37.9 + - + +
11211 PHE* 4.3 7.0 - - + -
11471 LEU* 3.6 23.8 - - + -
11491 PHE* 3.2 33.7 - - + -
11601 PHE* 5.1 6.5 - - + -
11611 ASP 3.2 3.8 - - - +
11621 VAL* 3.8 15.3 - - + -
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Residues in contact with VAL1075 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10731 LYS* 3.8 28.3 - - + +
10741 VAL* 1.3 80.3 - - - +
10761 MET* 1.3 71.5 + - - +
10771 SER* 3.7 10.7 + - - +
11161 SER* 6.0 0.9 - - - -
11171 TRP* 3.5 11.0 - - - +
11181 GLU* 4.7 7.6 - - + +
11601 PHE* 3.4 8.1 - - - -
11611 ASP* 2.7 44.7 + - + +
11631 LEU* 4.1 15.7 - - + -
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Residues in contact with MET1076 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10751 VAL* 1.3 74.9 - - - +
10771 SER* 1.3 64.4 - - - +
10781 GLY* 3.6 14.1 - - - -
10871 TRP* 3.6 7.6 - - + -
11131 GLU 3.6 17.5 - - - +
11151 HIS 3.4 31.9 - - - +
11161 SER* 2.9 30.5 - - - +
11171 TRP* 2.8 44.0 + - + +
11571 SER* 3.6 28.3 - - - +
11591 THR 3.5 5.4 - - - +
11601 PHE* 3.1 30.7 - - + -
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Residues in contact with SER1077 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10751 VAL* 3.7 12.6 + - - +
10761 MET* 1.3 76.7 - - - +
10781 GLY* 1.3 59.4 + - - +
11151 HIS 4.0 1.1 - - - -
11161 SER* 4.8 2.9 - - - -
11581 THR* 3.2 1.6 + - - -
11591 THR* 3.0 43.2 + - - +
11611 ASP* 4.6 10.7 + - - +
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Residues in contact with GLY1078 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10761 MET* 3.7 11.2 - - - -
10771 SER* 1.3 74.8 - - - +
10791 ASN* 1.3 61.8 + - - -
10801 ALA* 3.2 12.8 + - - +
11151 HIS* 2.7 26.9 + - - +
11561 GLN 3.7 4.5 - - - -
11581 THR* 3.4 10.8 - - - -
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Residues in contact with ASN1079 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10781 GLY* 1.3 69.2 - - - -
10801 ALA* 1.3 59.9 + - - +
10811 ALA* 2.9 23.8 + - - +
10821 VAL* 3.5 32.6 - - + +
10871 TRP* 3.8 12.5 - - - -
11151 HIS* 3.9 3.4 - - - -
11551 LYS 3.4 15.7 + - - +
11561 GLN* 2.9 24.5 + - - +
11581 THR* 3.5 15.8 + - + +
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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