Contacts of the strand formed by residues 732 - 742 (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 CYS 732 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726B TYR* 4.0 6.3 - - - -
727B GLN* 3.2 30.5 + - - +
730B SER* 3.4 31.0 - - - -
731B GLN* 1.3 80.0 - - - +
733B PHE* 1.3 62.4 + - - +
734B GLY 3.9 0.3 + - - -
793B ILE* 4.0 12.3 - - + -
794B ILE 3.0 22.4 - - - +
795B ASP* 4.2 2.7 - - - -
796B GLN* 4.3 3.1 - - - +
802B LEU* 4.9 4.9 - - + -
829B PHE* 4.0 3.5 - - - -
853B TYR* 4.0 21.8 - - - -
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Residues in contact with PHE 733 (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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363B CYS* 4.5 2.0 - - - -
365B VAL* 3.7 25.1 - - + -
367B LEU* 3.9 13.7 - - + -
376B VAL* 3.8 27.1 - - + -
387B LEU* 5.5 0.9 - - + -
724B ILE* 4.0 28.7 - - + -
725B CYS 3.2 14.1 - - - +
726B TYR* 3.7 17.3 - + + -
732B CYS* 1.3 73.1 - - - +
734B GLY* 1.3 59.6 + - - +
735B VAL* 4.2 6.1 - - + -
792B LEU 3.3 3.8 - - - +
793B ILE* 3.3 3.8 - - - +
794B ILE* 2.8 52.4 + - + +
796B GLN* 3.9 18.8 - - + -
799B PHE* 3.6 30.7 - + - -
829B PHE* 4.6 2.2 - - - -
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Residues in contact with GLY 734 (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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724B ILE* 3.5 0.3 - - - -
725B CYS 2.8 34.3 + - - -
732B CYS 3.9 1.4 + - - -
733B PHE* 1.3 73.0 - - - +
735B VAL* 1.3 64.1 + - - +
791B LEU* 3.8 12.3 - - - -
792B LEU 3.4 5.4 - - - -
793B ILE* 4.4 0.2 - - - -
816B LEU* 3.3 14.8 - - - +
829B PHE* 4.1 18.4 - - - -
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Residues in contact with VAL 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B CYS* 4.8 0.7 - - - -
387B LEU* 4.0 13.2 - - + -
717B LEU* 4.9 2.9 - - + -
721B PRO* 4.2 17.7 - - + -
723B LYS 3.6 8.1 - - - +
724B ILE* 3.6 28.0 - - + -
733B PHE* 4.2 5.2 - - + -
734B GLY* 1.3 78.6 - - - +
736B LEU* 1.3 72.0 + - - +
737B SER* 3.5 2.0 + - - +
790B ASN 3.3 2.1 - - - +
791B LEU* 3.5 4.9 - - - +
792B LEU* 2.7 49.6 + - + +
794B ILE* 3.8 26.0 - - + -
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Residues in contact with LEU 736 (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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721B PRO* 3.4 2.4 - - - +
722B ARG* 2.5 39.7 + - + -
723B LYS* 3.2 22.9 + - + +
735B VAL* 1.3 71.1 - - - +
737B SER* 1.3 56.1 + - - +
789B HIS* 6.4 0.2 - - - +
790B ASN 3.3 8.1 - - - +
791B LEU* 4.0 22.4 - - + -
807B PHE* 4.6 0.4 - - + -
813B ALA* 3.7 26.2 - - + +
814B LEU 4.1 1.6 - - - -
815B SER* 3.4 40.8 - - - +
816B LEU* 3.9 13.4 - - + +
831B VAL* 4.0 24.5 - - + -
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Residues in contact with SER 737 (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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717B LEU* 6.0 1.3 - - - -
719B GLU* 2.6 27.4 + - - -
720B SER 3.4 9.4 - - - -
721B PRO* 4.0 6.1 - - - -
722B ARG* 5.0 1.3 - - - +
735B VAL* 3.5 2.0 + - - -
736B LEU* 1.3 75.5 - - - +
738B SER* 1.3 61.6 + - - +
739B ARG 4.2 0.2 - - - -
757B SER* 3.5 4.9 + - - -
789B HIS* 3.5 8.8 + - - +
790B ASN* 2.9 45.8 + - - +
792B LEU* 3.8 20.6 - - - +
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Residues in contact with SER 738 (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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719B GLU* 3.3 3.9 + - - +
720B SER* 2.9 35.6 + - - -
722B ARG* 3.2 38.9 + - - -
737B SER* 1.3 79.6 - - - +
739B ARG* 1.3 61.5 + - - +
740B ILE* 4.0 4.2 + - - +
787B GLU* 3.4 17.2 + - - +
788B VAL 3.3 7.6 - - - -
789B HIS* 3.8 8.7 - - - -
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Residues in contact with ARG 739 (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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719B GLU* 3.8 21.2 + - + +
737B SER* 5.0 0.2 + - - -
738B SER* 1.3 74.5 - - - +
740B ILE* 1.3 60.3 + - - +
741B GLU* 3.3 30.5 + - + +
751B ALA* 5.9 2.6 - - - +
755B SER* 4.0 19.5 - - - +
757B SER* 3.2 23.8 + - - -
758B THR* 4.2 20.2 - - - +
787B GLU* 3.5 2.3 - - - -
788B VAL* 2.6 53.7 + - + +
790B ASN* 3.0 29.8 + - - +
806B GLN* 3.0 26.2 + - - -
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Residues in contact with ILE 740 (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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276B MET* 6.5 1.3 - - - -
382B PHE* 3.8 34.5 - - + -
720B SER* 5.4 0.4 - - - +
738B SER* 4.5 6.3 - - - +
739B ARG* 1.3 78.6 - - - +
741B GLU* 1.3 79.8 + - - +
752B LEU* 4.2 27.0 + - + +
785B GLU* 4.3 29.8 - - + +
786B VAL 4.2 9.4 - - - +
787B GLU* 4.3 19.5 - - + +
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Residues in contact with GLU 741 (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* 3.3 36.5 + - + +
740B ILE* 1.3 84.3 - - - +
742B VAL* 1.3 66.0 + - - +
749B THR* 3.2 24.8 + - + +
750B THR 2.9 34.3 + - - +
751B ALA* 3.6 19.5 - - - +
752B LEU* 5.0 2.9 - - - -
785B GLU* 3.5 8.3 - - - +
786B VAL 3.4 28.4 + - - +
788B VAL* 3.3 21.8 - - + +
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Residues in contact with VAL 742 (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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741B GLU* 1.3 78.1 - - - +
743B GLN* 1.3 73.5 + - + +
749B THR* 3.0 24.8 - - - +
750B THR* 3.5 13.6 + - - +
751B ALA 3.6 17.7 + - - +
752B LEU* 4.4 23.6 - - + -
784B GLU 3.5 5.4 - - - +
785B GLU* 5.6 6.3 - - + -
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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