Contacts of the strand formed by residues 801 - 806 (chain B) in PDB entry 3I8E
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 VAL 801 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B LEU* 5.4 3.8 - - + -
756B ALA* 3.8 36.3 - - + +
759B GLN* 5.1 4.0 - - + +
760B ALA* 3.8 7.1 - - + -
761B LEU* 3.1 29.2 + - - +
792B LEU* 4.1 23.3 - - + -
793B ILE 3.7 3.8 - - - +
794B ILE* 4.7 7.4 - - + -
799B PHE 5.0 3.4 - - - +
800B GLU* 1.3 74.9 - - - +
802B LEU* 1.3 65.3 + - - +
803B HIS 3.2 20.3 + - - +
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Residues in contact with LEU 802 (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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731B GLN 5.9 0.2 - - - +
732B CYS* 4.9 6.1 - - + -
761B LEU* 3.8 22.9 - - + +
762B SER* 3.0 23.9 + - - -
793B ILE* 2.8 13.1 + - + +
794B ILE 4.7 0.7 - - - -
795B ASP* 3.7 51.1 - - + +
798B THR* 4.8 0.7 - - - +
800B GLU* 3.5 7.4 + - + +
801B VAL* 1.3 71.6 - - - +
803B HIS* 1.3 58.3 + - - +
853B TYR* 3.4 34.3 + - + +
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Residues in contact with HIS 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760B ALA* 4.4 3.1 - - - -
762B SER* 3.5 19.8 + - - -
763B SER* 3.6 9.2 + - - -
764B SER* 2.8 43.5 + - - -
791B LEU 4.2 1.1 - - - -
792B LEU* 3.3 4.5 - - - -
793B ILE* 2.8 47.5 + - + -
801B VAL* 3.2 5.8 - - - +
802B LEU* 1.3 80.0 - - - +
804B ALA* 1.3 82.1 + - - +
805B HIS 3.8 2.3 + - - -
853B TYR* 4.2 10.5 - + + -
856B GLY 5.1 5.2 - - - -
858B LEU* 3.3 40.4 + - + +
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Residues in contact with ALA 804 (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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757B SER* 3.8 15.7 - - - +
760B ALA* 3.3 24.5 - - + -
762B SER 3.3 5.0 + - - +
763B SER* 3.6 7.8 - - - -
764B SER 3.3 17.5 + - - +
790B ASN* 4.3 5.4 - - - +
791B LEU 3.4 5.4 - - - -
792B LEU* 3.8 19.1 - - + -
803B HIS* 1.3 82.6 + - - +
805B HIS* 1.3 62.1 + - - +
806B GLN* 3.7 1.6 + - - +
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Residues in contact with HIS 805 (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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764B SER* 3.0 25.0 + - - +
765B VAL 3.5 22.0 - - - -
766B SER* 4.0 12.5 + - - -
767B SER 5.3 0.2 - - - -
790B ASN* 2.9 11.4 - - - +
791B LEU* 3.1 33.9 + - + +
803B HIS* 3.8 2.2 + - - -
804B ALA* 1.3 72.0 - - - +
806B GLN* 1.3 73.6 + - - +
807B PHE* 3.8 12.5 + + - -
847B ARG* 4.6 3.0 + - - -
851B PHE* 3.2 42.5 - + + -
858B LEU* 3.8 20.7 - - + +
860B THR* 4.2 12.8 - - + +
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Residues in contact with GLN 806 (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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739B ARG* 3.0 27.0 + - - +
764B SER 2.7 12.6 + - - +
765B VAL* 3.4 26.4 - - + +
766B SER* 2.7 31.7 + - - -
788B VAL* 3.8 19.3 - - + +
789B HIS 3.8 6.5 - - - +
790B ASN* 3.1 15.0 - - - +
804B ALA 5.0 1.3 - - - +
805B HIS* 1.3 75.1 - - - +
807B PHE* 1.3 72.9 + - - +
808B LEU 5.8 1.0 - - - -
809B GLN 5.9 0.4 - - - +
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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