Contacts of the strand formed by residues 862 - 869 (chain A) in PDB entry 5IFE
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 TRP 862 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786A ARG* 4.2 7.4 - - - -
802A THR* 3.6 17.3 - - + -
803A ASP 3.2 27.8 - - - -
804A HIS* 3.2 42.7 - + + -
806A ALA 2.8 16.9 - - - +
808A THR 4.1 2.6 + - - -
860A GLY 3.1 25.0 + - - -
861A GLN* 1.3 78.2 + - - +
863A ALA* 1.3 63.7 + - - +
884A GLN* 2.8 25.6 + - - +
885A ASN* 3.9 10.7 + - - -
886A GLU 4.1 14.4 - - - +
887A ALA* 3.5 17.3 - - + -
889A PHE* 4.0 17.9 - + - -
913A LEU* 3.1 53.0 + - + +
915A LEU* 4.5 11.2 - - + -
56B ALA 4.5 5.4 - - - -
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Residues in contact with ALA 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783A TYR* 3.6 31.5 - - + +
801A GLU 3.5 2.3 - - - +
802A THR* 3.3 2.7 - - - -
803A ASP 2.9 33.2 + - - -
806A ALA* 3.5 19.7 - - + -
807A TYR 3.6 11.2 - - - +
808A THR* 4.2 5.6 - - - +
862A TRP* 1.3 79.6 - - - +
864A SER* 1.3 59.7 + - - +
883A GLU 5.3 2.2 - - - -
884A GLN 4.6 2.0 - - - -
886A GLU 4.3 1.6 - - - -
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Residues in contact with SER 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A TYR* 4.5 0.2 - - - -
801A GLU 3.0 5.6 + - - -
802A THR* 2.7 25.2 + - - -
863A ALA* 1.3 72.8 - - - +
865A VAL* 1.3 72.7 + - - +
882A LEU* 3.3 34.4 + - - +
883A GLU 5.2 2.0 + - - +
886A GLU 3.3 22.6 + - - -
887A ALA* 3.7 1.3 - - - -
888A ALA* 3.0 25.4 + - - +
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Residues in contact with VAL 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782A GLN* 4.5 10.3 - - - +
783A TYR* 3.6 29.8 - - + -
799A ILE 3.6 0.9 - - - +
800A ILE* 3.5 3.9 - - - -
801A GLU* 2.9 38.0 + - + +
808A THR* 6.1 0.9 - - - +
864A SER* 1.3 81.6 + - - +
866A ILE* 1.3 75.6 + - - +
867A ARG* 4.8 6.5 - - + +
879A LEU* 3.6 25.6 - - + -
880A VAL 3.5 12.6 - - - +
881A GLN* 4.2 19.1 - - + -
882A LEU* 4.8 0.4 - - - -
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Residues in contact with ILE 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798A ILE* 4.1 17.0 - - + -
799A ILE 3.4 8.1 - - - +
800A ILE* 4.5 6.7 - - + -
864A SER* 5.9 0.2 - - - +
865A VAL* 1.3 81.4 - - - +
867A ARG* 1.3 62.7 + - - +
878A ASP 4.8 0.2 - - - -
879A LEU* 3.6 1.2 - - - -
880A VAL* 2.9 41.7 + - + +
882A LEU* 4.3 20.2 - - + -
905A VAL* 5.4 0.7 - - + -
907A VAL* 3.6 41.5 - - + -
926A TYR* 5.2 1.1 - - + -
928A TYR* 3.9 29.2 - - + +
937A LEU* 3.7 22.4 - - + -
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Residues in contact with ARG 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780A PRO 5.2 2.6 + - - -
781A LEU* 3.9 10.1 - - - +
782A GLN* 3.3 40.4 - - - +
797A LEU 3.4 1.2 - - - +
798A ILE* 3.4 5.2 - - - +
799A ILE* 2.9 43.0 + - + +
801A GLU* 2.7 45.0 + - - +
865A VAL* 4.8 2.4 - - + +
866A ILE* 1.3 76.4 - - - +
868A VAL* 1.3 66.1 + - - +
869A MET* 4.0 22.3 + - - +
876A THR* 3.2 44.2 + - - +
878A ASP 3.5 5.2 - - - +
879A LEU* 3.4 25.0 - - + +
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Residues in contact with VAL 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796A ASN* 4.8 4.5 - - + -
797A LEU 3.3 3.8 - - - +
798A ILE* 3.6 27.1 - - + -
867A ARG* 1.3 73.1 - - - +
869A MET* 1.3 54.0 + - - +
876A THR* 3.3 2.9 + - - -
877A LEU* 2.4 46.0 + - + -
878A ASP* 2.9 31.5 + - + +
930A LEU* 4.6 2.7 - - + -
934A GLY 3.3 28.3 - - - +
935A GLU 4.6 2.2 - - - +
937A LEU* 3.6 33.4 - - + +
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Residues in contact with MET 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A LEU* 3.6 33.7 - - + -
779A PHE* 3.7 25.4 - - + -
780A PRO 4.6 4.9 - - - +
781A LEU* 4.2 10.1 - - + -
796A ASN* 3.5 4.8 - - - +
797A LEU* 2.9 36.2 + - + +
799A ILE* 4.5 11.7 - - + -
867A ARG* 4.0 26.4 - - - +
868A VAL* 1.3 74.4 - - - +
870A ASN* 1.3 75.3 + - - +
871A PRO* 3.5 1.6 - - + +
873A GLN 5.0 0.2 - - - +
874A GLY 3.9 18.8 - - - +
875A ASN 3.6 9.6 - - - +
876A THR* 4.5 5.6 - - - -
877A LEU* 4.0 0.9 - - - +
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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