Contacts of the strand formed by residues 744 - 749 (chain B) in PDB entry 1B70
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 ALA 744 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697B LEU 3.9 2.2 - - - -
698B ALA* 4.9 2.9 - - - +
727B LEU* 3.0 8.3 - - - +
728B PHE* 2.6 54.5 + - + -
729B ASP* 2.4 59.1 + - + +
730B LEU* 4.6 0.2 - - - +
743B LEU 1.3 62.7 - - - +
745B PHE* 1.3 57.8 + - - +
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Residues in contact with PHE 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B ARG 3.8 0.5 - - - +
697B LEU* 2.7 41.0 + - + +
699B VAL* 4.6 7.2 - - + -
707B TYR* 4.0 22.2 - + - -
710B VAL* 4.5 0.7 - - + -
711B GLU* 4.3 6.3 - - - -
714B VAL* 3.8 40.2 - - + -
725B LEU* 4.1 19.5 - - + -
726B ALA 3.1 9.6 - - - +
727B LEU* 3.4 29.6 - - + -
728B PHE* 2.9 4.8 - - - -
743B LEU* 3.1 30.0 + - + +
744B ALA* 1.3 78.4 - - - +
746B HIS* 1.3 60.5 + - - +
747B LEU* 3.1 21.7 + - + +
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Residues in contact with HIS 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694B PHE* 6.5 1.6 - + - -
695B ARG 3.6 14.1 - - - -
696B ASP* 4.9 3.9 - - + +
724B SER* 4.4 1.3 - - - -
725B LEU* 3.6 3.5 + - - -
726B ALA* 2.9 39.0 + - + +
728B PHE* 2.9 52.9 - + + +
745B PHE* 1.3 72.6 - - - +
747B LEU* 1.3 64.0 - - - +
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Residues in contact with LEU 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693B ALA 4.0 1.1 - - - -
694B PHE* 3.3 6.4 - - - +
695B ARG* 2.8 51.1 + - + +
697B LEU* 4.2 21.8 - - + -
714B VAL* 5.5 8.5 - - + -
718B ALA* 5.2 5.6 - - + -
722B LEU* 4.1 9.0 - - + -
724B SER* 4.0 6.3 - - - +
725B LEU* 5.0 8.5 - - + -
745B PHE* 3.1 45.1 - - + +
746B HIS* 1.3 78.2 - - - +
748B ARG* 1.3 65.3 + - - +
749B PHE* 3.9 25.8 - - + -
765B VAL* 6.6 0.2 - - + -
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Residues in contact with ARG 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692B ALA* 4.0 4.6 - - + +
693B ALA 3.1 3.6 - - - -
694B PHE* 3.5 50.5 - - + -
722B LEU* 3.3 6.4 - - - +
723B GLU* 2.8 43.8 + - - +
724B SER* 3.3 34.8 + - - +
746B HIS 6.4 0.2 - - - -
747B LEU* 1.3 75.5 - - - +
749B PHE* 1.3 68.5 + - - +
750B ARG* 5.9 1.4 - - - +
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Residues in contact with PHE 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691B PRO 4.4 0.2 - - - +
692B ALA* 2.7 11.6 - - - +
693B ALA* 2.7 49.7 + - + +
695B ARG* 4.6 11.2 - - + -
718B ALA* 3.5 27.8 - - + -
721B TYR* 3.0 29.8 - - + -
722B LEU* 3.5 23.1 - - + -
723B GLU* 3.8 3.1 - - - +
747B LEU* 3.9 29.2 - - + -
748B ARG* 1.3 91.8 - - - +
750B ARG* 1.3 62.5 + - - +
756B LEU* 3.6 16.7 - - + +
761B VAL* 5.7 7.0 - - + -
764B ALA* 5.4 6.5 - - + -
765B VAL* 6.1 5.2 - - - -
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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
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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