Contacts of the strand formed by residues 1115 - 1125 (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 HIS1115 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10761 MET* 3.4 7.3 - - - +
10781 GLY* 2.7 33.5 + - - +
10791 ASN 3.9 10.1 - - - +
10801 ALA* 4.6 16.3 - - + +
10821 VAL 3.1 23.6 + - - -
10841 ARG* 4.1 33.4 + - + +
10871 TRP* 3.3 37.5 - + - -
11131 GLU 3.4 0.4 + - - -
11141 PRO* 1.3 70.2 + - + +
11161 SER* 1.3 62.7 + - - +
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Residues in contact with SER1116 (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* 6.0 1.3 - - - -
10761 MET* 2.9 16.3 - - - +
10771 SER* 4.8 2.9 - - - -
11131 GLU* 3.7 9.8 - - - +
11141 PRO 2.8 19.5 + - - +
11151 HIS* 1.3 79.9 - - - +
11171 TRP* 1.3 66.6 + - - +
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Residues in contact with TRP1117 (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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10741 VAL* 3.9 23.8 - - + -
10751 VAL* 3.5 6.2 - - - +
10761 MET* 2.8 62.1 + - + +
10911 VAL* 2.7 40.7 - - + +
10931 VAL* 4.1 18.4 - - + -
11111 LYS* 3.9 37.9 + - + +
11131 GLU* 3.7 30.3 - - + +
11161 SER* 1.3 75.7 - - - +
11181 GLU* 1.3 65.7 + - - +
11191 LEU* 4.2 13.9 - - + -
11491 PHE* 4.3 8.3 - + - -
11571 SER* 4.9 0.6 + - - -
11601 PHE* 3.8 21.5 - + - -
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Residues in contact with GLU1118 (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* 3.4 38.8 + - + +
10741 VAL 3.7 5.6 - - - +
10751 VAL* 4.7 7.9 - - + +
11111 LYS* 3.9 20.6 + - - +
11171 TRP* 1.3 75.7 - - - +
11191 LEU* 1.3 65.7 + - - +
11201 ILE* 3.7 17.9 - - + +
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Residues in contact with LEU1119 (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 3.9 0.5 - - - +
10731 LYS* 3.5 4.9 - - - -
10741 VAL* 3.3 40.6 + - + +
10931 VAL* 4.6 15.7 - - + -
11091 TRP* 3.5 54.1 - - + +
11111 LYS* 4.9 10.8 - - + -
11171 TRP* 4.2 12.3 - - + -
11181 GLU* 1.3 79.0 - - - +
11201 ILE* 1.3 66.3 + - - +
11211 PHE* 3.7 28.5 + - + -
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Residues in contact with ILE1120 (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* 3.7 23.3 - - + -
10711 MET* 4.8 9.2 - - + -
10721 VAL 3.5 10.8 - - - +
10731 LYS* 3.0 37.2 - - + +
11181 GLU* 3.7 22.9 - - + +
11191 LEU* 1.3 77.7 - - - +
11211 PHE* 1.3 67.7 - - - +
11221 PRO* 4.6 1.2 - - - +
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Residues in contact with PHE1121 (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* 5.2 0.2 - - + -
10711 MET* 4.1 4.9 - - - -
10721 VAL* 3.0 55.3 + - + +
10741 VAL* 4.3 2.9 - - + -
10951 LEU* 3.5 24.2 - - + -
11091 TRP* 3.5 43.1 - + + +
11191 LEU* 3.7 33.0 - - + -
11201 ILE* 1.3 74.6 - - - +
11221 PRO* 1.3 84.3 - - + +
11231 ILE* 3.5 13.0 - - + -
11471 LEU* 3.8 23.6 - - + -
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Residues in contact with PRO1122 (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* 6.1 3.6 - - + -
10701 LEU 3.8 1.6 - - - +
10711 MET* 3.7 28.4 - - + -
10951 LEU* 5.6 2.1 - - - +
11201 ILE 4.6 1.1 - - - +
11211 PHE* 1.3 98.0 - - + +
11231 ILE* 1.3 66.8 + - - +
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Residues in contact with ILE1123 (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* 3.8 32.5 - - + -
10351 LEU* 4.7 4.0 - - + -
10691 CYS* 3.4 5.5 - - - +
10701 LEU* 3.0 64.0 + - + +
10721 VAL* 3.9 14.4 - - + -
10951 LEU* 4.4 10.5 - - + -
11211 PHE* 3.5 27.4 - - + +
11221 PRO* 1.3 80.4 - - - +
11241 GLU* 1.3 59.8 + - - +
11251 VAL* 5.4 1.3 - - + -
11451 TRP* 4.2 26.7 - - + +
11641 LEU* 5.6 1.1 - - + -
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Residues in contact with GLU1124 (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* 3.3 8.9 - - - +
10691 CYS* 3.5 27.5 - - - -
11221 PRO* 6.4 0.2 - - + -
11231 ILE* 1.3 75.0 - - - +
11251 VAL* 1.3 65.5 - - - +
11261 CYS* 3.3 32.1 + - - +
11451 TRP* 3.1 24.4 + - - +
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Residues in contact with VAL1125 (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* 3.5 39.9 - - + -
10661 LYS* 3.0 32.8 - - + +
10671 LYS* 3.6 7.8 - - - +
10681 GLY* 2.6 38.7 + - - +
10701 LEU* 4.8 3.4 - - + -
11231 ILE* 5.4 2.5 - - + -
11241 GLU* 1.3 73.4 - - - +
11261 CYS* 1.3 62.5 + - - +
11311 GLY 3.9 1.9 - - - +
11331 GLU* 3.8 27.1 - - + +
11451 TRP* 4.4 6.1 - - + +
11701 PHE* 4.2 11.9 - - + -
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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