Contacts of the strand formed by residues 855 - 863 (chain B) in PDB entry 6AHU
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 855 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712B THR* 4.3 6.7 - - - +
804B CYS* 3.3 15.9 - - + +
806B LEU* 5.1 8.3 - - + -
852B PHE* 4.1 16.6 + - + +
854B ARG* 1.3 78.3 - - - +
856B LEU* 1.3 66.5 + - - +
986B SER* 3.6 23.0 + - - -
987B LEU* 3.7 33.1 + - + +
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Residues in contact with LEU 856 (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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664B PRO* 3.7 27.8 - - + -
708B TRP* 4.7 19.7 - - + -
712B THR* 4.3 20.2 - - + -
803B LEU* 5.3 7.2 - - + -
804B CYS 2.8 14.7 + - - +
805B VAL* 3.3 31.5 - - + +
806B LEU 3.7 1.9 + - - -
855B ALA* 1.3 80.0 - - - +
857B VAL* 1.3 59.8 + - - +
984B PHE* 3.6 38.3 - - + -
985B VAL 3.3 16.6 - - - +
986B SER* 4.4 2.7 - - - +
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Residues in contact with VAL 857 (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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805B VAL* 5.5 0.4 - - - -
806B LEU* 3.8 28.9 - - + +
812B LEU* 4.2 21.8 - - + -
815B LEU* 4.9 6.1 - - + -
856B LEU* 1.3 77.1 - - - +
858B TRP* 1.3 80.9 + - + +
859B VAL* 5.2 3.1 - - + -
984B PHE* 4.3 2.9 - - - -
985B VAL* 2.8 40.5 + - + +
986B SER* 4.6 1.1 - - - +
987B LEU* 3.7 33.7 - - + -
990B LEU* 5.2 5.4 - - + -
1022B ILE* 5.3 6.1 - - + -
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Residues in contact with TRP 858 (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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607B THR* 4.8 8.3 - - + -
655B ARG* 3.7 20.4 - - + -
657B PRO* 5.3 17.8 - - + +
805B VAL* 5.4 11.0 - - + +
806B LEU 5.4 3.7 + - - -
807B ARG* 5.7 6.8 - - + +
812B LEU* 5.0 10.9 - - + +
856B LEU 4.4 0.2 + - - -
857B VAL* 1.3 89.5 - - + +
859B VAL* 1.3 67.9 + - - +
860B SER* 3.4 29.6 - - - -
982B LEU* 4.4 6.7 - - + -
983B GLY 3.4 10.8 - - - +
984B PHE* 3.6 30.3 - + + -
1022B ILE* 4.2 9.8 - - + +
1023B GLU* 3.8 27.6 - - + -
1024B VAL* 3.7 22.9 - - + -
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Residues in contact with VAL 859 (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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857B VAL* 3.9 1.1 + - + +
858B TRP* 1.3 80.7 - - - +
860B SER* 1.3 75.9 + - - +
861B LEU* 3.8 12.0 - - + +
982B LEU* 3.7 4.1 - - - +
983B GLY 2.9 31.4 + - - +
985B VAL* 3.7 32.8 - - + -
990B LEU* 4.5 6.1 - - + -
1020B ILE* 3.7 33.2 - - + -
1021B ALA 4.7 0.4 - - - +
1022B ILE* 3.7 25.1 - - + -
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Residues in contact with SER 860 (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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655B ARG* 3.3 35.0 - - - +
858B TRP* 3.4 19.2 - - - -
859B VAL* 1.3 75.5 - - - +
861B LEU* 1.3 58.9 + - - +
981B ALA 4.3 2.9 - - - -
982B LEU* 3.4 16.4 - - - +
1019B ARG 4.1 0.2 - - - +
1021B ALA* 3.0 39.5 + - - +
1022B ILE* 5.2 0.4 - - - +
1023B GLU* 5.5 7.8 - - - +
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Residues in contact with LEU 861 (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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859B VAL* 3.8 16.4 - - + +
860B SER* 1.3 76.2 - - - +
862B SER* 1.3 60.9 + - - +
863B LEU* 6.4 0.2 - - + -
875B ILE* 3.8 29.4 - - + -
966B PHE 5.8 0.4 - - - +
967B VAL* 4.6 5.6 - - + -
980B GLU* 3.1 11.9 + - - +
981B ALA* 3.4 53.1 + - + +
982B LEU* 4.0 2.2 - - - +
983B GLY 4.5 3.4 - - - +
1005B VAL 5.5 2.0 - - - +
1007B LEU* 3.8 10.3 - - + -
1018B ALA* 3.7 22.0 - - + -
1019B ARG 3.4 13.0 - - - +
1020B ILE* 4.4 15.5 - - + -
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Residues in contact with SER 862 (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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655B ARG* 5.7 0.7 - - - -
861B LEU* 1.3 74.1 - - - +
863B LEU* 1.3 66.8 + - - +
976B VAL* 5.0 3.1 - - - +
980B GLU* 2.6 31.2 + - - -
1018B ALA* 3.3 3.1 - - - -
1019B ARG* 2.7 49.0 + - - +
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Residues in contact with LEU 863 (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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861B LEU* 4.3 0.8 - - + -
862B SER* 1.3 81.8 + - - +
864B LEU* 1.3 64.2 + - - +
865B SER 4.8 2.5 - - - +
867B GLY* 3.6 35.0 - - - -
868B SER 3.9 1.3 - - - +
869B PRO* 3.7 25.6 - - + -
978B CYS* 3.7 19.5 - - - +
979B GLY* 3.1 22.3 + - - +
981B ALA* 5.8 2.7 - - + +
1007B LEU* 3.8 22.7 - - + -
1016B ARG* 4.6 10.8 - - + +
1017B PHE 3.4 20.0 - - - +
1018B ALA* 3.7 15.7 - - + +
1019B ARG* 5.7 0.2 - - - -
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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