Contacts of the strand formed by residues 1156 - 1173 (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 GLN1156 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10781 GLY* 3.7 1.6 - - - -
10791 ASN* 2.9 29.1 + - - +
10821 VAL* 3.3 30.9 - - + +
10861 ASP 2.9 27.9 + - - -
10871 TRP* 3.5 20.5 - - + +
10881 ALA* 2.8 42.2 + - - +
10891 SER* 3.5 5.2 - - - -
11531 ASN* 3.0 22.1 + - - +
11551 LYS* 1.3 79.9 - - - +
11571 SER* 1.3 54.0 + - - +
11581 THR* 2.9 16.9 + - - +
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Residues in contact with SER1157 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10161 THR* 4.1 1.4 + - - -
10761 MET* 3.6 24.9 - - - +
10871 TRP* 3.5 15.3 - - - -
10891 SER* 2.7 27.3 + - - -
10901 LEU 4.7 1.8 + - - -
10911 VAL* 5.0 2.7 - - - +
11171 TRP* 4.9 3.5 + - - -
11511 VAL* 3.2 31.4 - - - +
11531 ASN 3.2 2.2 + - - -
11541 PRO 3.8 5.5 - - - +
11561 GLN* 1.3 74.2 - - - +
11581 THR* 1.4 60.4 - - - +
11591 THR 3.9 1.3 - - - -
11601 PHE* 3.7 13.5 - - - -
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Residues in contact with THR1158 (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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10151 ARG* 3.5 27.8 + - - +
10161 THR* 2.4 37.0 + - - -
10771 SER 3.2 9.0 + - - -
10781 GLY* 3.4 10.9 - - - -
10791 ASN* 3.6 13.7 - - + +
11541 PRO 3.6 10.1 - - - +
11551 LYS* 3.5 20.6 - - - +
11561 GLN 2.9 15.8 + - - +
11571 SER* 1.4 74.2 - - - +
11591 THR* 1.3 75.5 + - - +
11601 PHE* 4.2 0.9 + - - -
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Residues in contact with THR1159 (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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10131 THR* 5.3 7.4 - - + -
10141 VAL 3.8 9.2 - - - +
10151 ARG* 3.8 23.9 + - + -
10761 MET* 3.5 3.1 - - - +
10771 SER* 3.0 44.5 + - - +
11581 THR* 1.3 91.2 + - - +
11601 PHE* 1.4 83.8 + - - +
11611 ASP* 4.8 9.6 - - + +
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Residues in contact with PHE1160 (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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10121 ALA* 5.3 0.3 - - - +
10131 THR* 3.2 2.9 + - - -
10141 VAL* 2.6 49.4 + - + +
10161 THR* 4.5 9.9 - - - -
10301 PHE* 3.3 35.2 - + + -
10471 TRP* 6.3 0.2 - + - -
10741 VAL* 5.1 7.2 - - + -
10751 VAL 3.4 4.9 - - - -
10761 MET* 3.1 31.2 - - + -
10911 VAL* 3.8 20.2 - - + -
11171 TRP* 3.8 21.5 - + - -
11491 PHE* 5.1 4.7 - + - -
11511 VAL* 3.6 27.6 - - + -
11571 SER* 3.7 23.3 - - - -
11591 THR* 1.4 79.3 - - - +
11611 ASP* 1.3 60.4 + - - +
11621 VAL* 5.4 2.7 - - + -
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Residues in contact with ASP1161 (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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10101 GLN* 4.6 12.8 - - - +
10121 ALA 3.2 5.8 - - - +
10131 THR* 2.4 28.5 + - - +
10521 GLN* 4.6 0.2 - - - +
10731 LYS 3.5 1.6 - - - +
10741 VAL* 3.2 4.1 - - - +
10751 VAL* 2.7 55.5 + - + +
10771 SER* 4.6 9.7 + - - +
11591 THR* 4.8 8.9 - - + +
11601 PHE* 1.3 72.5 - - - +
11621 VAL* 1.3 63.8 + - - +
11631 LEU* 4.0 8.0 + - + +
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Residues in contact with VAL1162 (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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10101 GLN* 4.0 0.9 - - - +
10111 MET* 2.9 24.9 + - - +
10121 ALA* 2.6 62.0 + - + +
10141 VAL* 6.2 0.2 - - + -
10301 PHE* 5.8 1.6 - - + -
10321 VAL* 4.4 18.6 - - + -
10341 LEU* 4.9 3.6 - - + -
10721 VAL* 4.8 8.3 - - + -
10731 LYS 3.2 6.3 - - - +
10741 VAL* 3.8 22.4 - - + -
11471 LEU* 4.8 3.1 - - + -
11491 PHE* 4.6 6.7 - - + -
11601 PHE* 5.4 3.4 - - + -
11611 ASP* 1.3 75.7 - - - +
11631 LEU* 1.3 71.3 - - - +
11641 LEU* 4.5 6.1 - - + -
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Residues in contact with LEU1163 (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* 4.7 17.0 - - + -
10091 ASN* 4.0 9.4 - - - +
10101 GLN* 3.9 32.3 - - + +
10111 MET 4.4 0.9 - - - +
10721 VAL* 3.4 3.6 - - - +
10731 LYS* 2.5 81.2 + - + +
10751 VAL* 4.1 14.6 - - + -
11611 ASP* 4.9 9.4 - - + +
11621 VAL* 1.3 77.7 - - - +
11641 LEU* 1.3 60.6 + - - +
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Residues in contact with LEU1164 (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 7.1 - - - -
10091 ASN* 2.9 34.2 + - - +
10111 MET* 3.6 37.0 - - + -
10341 LEU* 4.0 12.6 - - + +
10561 ILE* 3.6 37.5 - - + +
10571 SER 5.3 0.2 - - - +
10601 LEU* 3.8 17.7 - - + -
10701 LEU* 5.2 6.3 - - + -
10711 MET 2.6 21.5 - - - +
10721 VAL* 3.7 23.6 - - + -
11231 ILE* 5.6 2.5 - - + -
11621 VAL* 4.5 3.8 - - + -
11631 LEU* 1.3 72.9 - - - +
11651 GLY* 1.3 60.9 - - - +
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Residues in contact with GLY1165 (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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10071 VAL 5.6 1.6 - - - -
10081 TRP* 3.6 17.4 - - - -
10091 ASN* 5.0 2.9 - - - -
10561 ILE* 4.4 5.8 - - - -
10701 LEU* 3.3 7.6 - - - +
10711 MET* 2.5 45.2 + - - -
11641 LEU* 1.3 76.9 - - - +
11661 ILE* 1.3 61.4 + - - -
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Residues in contact with ILE1166 (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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10091 ASN* 5.9 2.5 - - - +
10591 LEU* 4.6 2.9 - - + -
10701 LEU* 4.1 11.0 - - + -
10711 MET* 5.2 2.6 - - - +
11651 GLY* 1.3 76.5 - - - -
11671 SER* 1.3 79.7 + - - +
11681 GLN* 4.1 3.3 + - - -
11701 PHE* 3.7 32.3 - - + -
20022 VAL* 4.2 22.2 - - + -
20032 LEU* 3.6 25.2 - - + +
20562 MET* 3.8 34.3 - - + -
21772 LEU* 5.5 9.9 - - + -
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Residues in contact with SER1167 (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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10691 CYS* 2.2 44.8 + - - +
11661 ILE* 1.3 86.2 - - - +
11681 GLN* 1.3 59.0 + - - +
11691 ASN* 2.4 41.9 + - - -
11701 PHE* 3.1 12.5 + - - +
20032 LEU* 3.8 4.9 - - - +
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Residues in contact with GLN1168 (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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10011 SER* 3.5 30.0 + - - +
10021 ILE 3.4 8.9 + - - +
10031 SER* 3.3 29.6 - - - -
11661 ILE 5.2 2.2 + - - -
11671 SER* 1.3 74.5 + - - +
11691 ASN* 1.3 57.6 + - + +
11701 PHE 3.6 1.3 + - - -
20012 CYS* 3.7 18.2 - - - -
20032 LEU* 3.9 20.9 - - + +
20042 ASN* 5.3 1.0 - - - +
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Residues in contact with ASN1169 (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* 3.5 9.9 - - - +
10681 GLY* 3.3 19.6 - - - -
10691 CYS* 3.6 15.6 - - - +
11671 SER* 2.4 34.6 + - - -
11681 GLN* 1.3 78.1 - - + +
11701 PHE* 1.3 57.5 + - - +
11711 GLU* 3.7 5.1 + - - +
20012 CYS* 4.7 5.4 - - - -
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Residues in contact with PHE1170 (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* 4.8 0.4 - - + -
10591 LEU* 4.5 4.5 - - + -
10601 LEU* 3.6 20.2 - - + -
10631 ALA* 6.1 0.2 - - + -
10661 LYS* 4.1 20.4 - - + -
10671 LYS 3.4 5.4 - - - -
10681 GLY* 4.0 15.9 - - - -
10691 CYS 4.0 3.6 - - - +
10701 LEU* 3.0 48.5 - - + -
11251 VAL* 4.2 14.8 - - + -
11661 ILE* 3.7 23.1 - - + -
11671 SER 3.1 14.0 + - - +
11681 GLN 3.6 1.0 - - - -
11691 ASN* 1.3 73.7 - - - +
11711 GLU* 1.3 63.2 + - - +
11721 ILE* 3.5 33.0 - - + -
20012 CYS* 3.7 1.9 - - - -
20022 VAL* 3.2 31.3 + - + +
20032 LEU* 6.0 0.2 - - - +
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Residues in contact with GLU1171 (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* 3.7 0.7 - - - -
10671 LYS* 2.8 57.0 + - + +
11321 PHE* 3.4 32.5 - - + -
11691 ASN 4.4 5.6 - - - +
11701 PHE* 1.3 77.7 - - - +
11721 ILE* 1.3 63.5 - - - +
20012 CYS* 4.3 19.5 - - - +
31812 THR* 3.1 23.2 + - - +
31822 TYR 3.1 9.2 - - - +
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Residues in contact with ILE1172 (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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10591 LEU* 3.3 32.5 - - + -
10631 ALA* 3.6 22.9 - - + -
10651 TRP 3.0 15.7 - - - +
10661 LYS* 4.8 1.6 - - + -
11321 PHE* 4.3 2.2 - - - -
11701 PHE* 3.5 32.3 - - + -
11711 GLU* 1.3 80.8 - - - +
11731 ALA* 1.3 61.1 + - - +
20022 VAL* 4.0 11.2 - - + -
20492 MET* 3.2 30.3 - - + -
20532 VAL* 4.7 2.5 - - + -
31812 THR* 3.7 1.6 - - - -
31822 TYR* 2.8 40.1 + - + +
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Residues in contact with ALA1173 (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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10641 ALA 5.0 0.2 - - - -
10651 TRP* 2.7 41.9 + - - +
11321 PHE* 4.4 4.7 - - + -
11721 ILE* 1.3 83.7 - - - +
11741 GLY* 1.3 61.4 - - - +
20492 MET* 3.5 9.6 - - - -
31312 PRO* 4.1 15.0 - - + +
31322 CYS* 4.3 11.4 - - - -
31802 ARG 3.6 22.0 - - - +
31812 THR* 3.9 6.7 - - - -
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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