Contacts of the strand formed by residues 899 - 907 (chain C) in PDB entry 3N1Q
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 SER 899 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B ASN* 3.6 28.8 - - - +
868C PRO* 3.8 0.5 - - - +
869C THR* 2.8 40.7 + - - +
898C THR* 1.3 84.0 - - - +
900C TYR* 1.3 67.2 + - - +
920C ILE* 3.6 15.2 - - - +
921C CYS 3.4 11.4 + - - -
922C GLU* 4.0 11.2 + - - +
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Residues in contact with TYR 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843C ILE* 4.5 7.2 - - + -
866C TYR* 4.7 10.5 - + + -
867C ARG 3.2 25.8 - - - +
868C PRO* 4.1 13.2 - - + -
869C THR* 2.9 9.4 + - - -
894C LEU* 3.8 46.3 - - + +
895C GLN* 3.2 20.3 + - - +
898C THR* 3.2 41.7 - - + -
899C SER* 1.3 73.3 - - - +
901C ASP* 1.3 63.4 + - - +
902C ILE* 4.5 10.4 - - + +
919C MET 3.7 0.2 - - - +
920C ILE* 3.3 7.8 - - - +
921C CYS 2.7 34.5 + - - +
923C THR* 4.3 4.0 - - + -
83E PRO* 3.9 23.9 - - + +
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Residues in contact with ASP 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LYS* 2.9 29.2 + - - -
90B GLU* 4.6 3.6 - - - -
866C TYR* 3.2 7.4 - - - -
867C ARG* 2.7 64.3 + - - +
869C THR* 3.3 22.3 + - - +
877C TYR* 3.5 22.6 - - + +
900C TYR* 1.3 74.6 - - - +
902C ILE* 1.3 60.0 + - - +
903C LYS 4.2 0.4 - - - -
918C VAL* 4.3 6.3 - - + -
919C MET 3.5 4.3 - - - -
920C ILE* 3.7 8.7 - - - +
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Residues in contact with ILE 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832C ILE* 3.7 10.2 - - + +
835C THR* 4.3 14.1 - - + -
843C ILE* 4.2 27.6 - - + -
844C MET 5.4 0.2 - - - +
845C LEU* 4.1 25.4 - - + -
864C ILE* 4.8 6.3 - - + -
865C TYR 3.5 8.7 - - - +
866C TYR* 4.4 10.1 - - + -
891C ILE* 4.2 15.7 - - + -
894C LEU* 6.4 0.4 - - + -
900C TYR* 4.5 9.4 - - + +
901C ASP* 1.3 80.0 - - - +
903C LYS* 1.3 64.4 + - - +
917C ASN 3.7 2.4 - - - +
918C VAL* 3.4 3.5 - - - +
919C MET* 2.7 44.5 + - + +
921C CYS* 4.5 10.3 - - + +
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Residues in contact with LYS 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLU 4.2 8.7 + - - +
92B ASN* 4.2 5.9 - - - +
832C ILE* 4.3 2.0 - - - -
864C ILE* 3.9 0.3 - - - -
865C TYR* 2.9 33.5 + - + +
874C ASP* 3.7 28.5 + - - +
877C TYR* 3.6 37.4 - - + +
901C ASP 4.2 0.4 - - - -
902C ILE* 1.3 76.9 - - - +
904C MET* 1.3 62.0 + - - +
915C PHE* 3.9 48.8 - - + -
916C SER* 3.9 11.7 - - - +
917C ASN 4.1 0.9 - - - +
918C VAL* 3.8 28.7 - - + -
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Residues in contact with MET 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830C PRO* 4.0 8.3 - - + -
832C ILE* 4.0 13.9 - - + -
845C LEU* 4.8 4.3 - - + -
847C TRP* 3.5 52.0 - - + +
862C PHE* 3.5 43.3 - - + -
863C TYR 3.1 17.9 - - - +
864C ILE* 4.2 13.7 - - + -
865C TYR* 4.5 1.6 - - - -
903C LYS* 1.3 74.8 - - - +
905C GLN* 1.3 63.8 + - - +
915C PHE* 3.6 4.8 - - - -
916C SER* 2.8 52.0 + - - +
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Residues in contact with GLN 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830C PRO* 3.7 13.5 - - - -
862C PHE* 3.4 3.8 - - - +
863C TYR* 2.7 42.3 + - + +
865C TYR* 3.2 30.7 + - + -
904C MET* 1.3 79.8 - - - +
906C CYS* 1.3 59.5 + - - +
912C GLU* 3.5 23.0 - - - +
913C SER 2.6 34.3 + - - +
914C GLU* 3.8 7.1 - - - +
915C PHE* 3.6 29.8 - - + +
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Residues in contact with CYS 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830C PRO* 3.7 4.1 - - + +
849C TYR* 3.4 35.7 - - + -
859C ILE* 4.1 11.4 - - + -
861C GLY 3.5 7.4 - - - +
862C PHE* 3.5 26.7 - - + -
905C GLN* 1.3 75.7 - - - +
907C PHE* 1.3 62.1 + - - +
912C GLU* 3.3 4.6 - - - +
913C SER* 2.9 52.7 + - - -
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Residues in contact with PHE 907 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859C ILE* 3.8 3.6 - - - +
860C GLN* 3.0 44.1 + - + -
861C GLY* 3.0 49.1 + - - +
862C PHE 3.4 10.5 - - - -
863C TYR* 3.3 61.5 - + + +
881C VAL* 4.2 13.9 - - + -
882C VAL 4.8 0.2 - - - -
906C CYS* 1.3 77.8 - - - +
908C ASN* 1.3 67.2 + - - +
911C GLY 3.2 13.9 - - - +
912C GLU* 3.9 4.3 - - + +
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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