Contacts of the strand formed by residues 890 - 898 (chain K) in PDB entry 5ANC
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 890 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694K GLU 3.8 20.9 - - - +
696K ILE* 3.9 22.7 - - + +
755K ALA* 3.9 22.9 - - + -
756K MET 3.6 14.8 - - - +
758K LEU* 4.2 7.6 - - - +
763K THR* 4.9 0.2 - - - +
833K PRO* 3.5 29.2 - - - +
834K ASN* 3.8 22.2 + - - +
887K LEU* 4.4 7.2 - - + -
888K MET* 3.9 6.7 - - - +
889K GLY* 1.3 84.8 - - - +
891K CYS* 1.3 66.9 + - - +
892K PHE* 4.0 3.6 - - + +
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Residues in contact with CYS 891 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756K MET* 3.6 34.4 + - - -
757K PRO 3.3 26.0 - - - -
758K LEU* 3.7 21.9 - - + +
796K THR* 4.7 2.2 - - + -
806K LYS* 3.4 34.1 - - - +
810K HIS* 4.7 1.3 - - - -
833K PRO 4.3 6.3 - - - +
834K ASN* 4.7 0.2 - - - +
835K ILE* 5.2 0.4 - - + +
890K VAL* 1.3 75.3 - - - +
892K PHE* 1.3 65.8 + - - +
893K VAL* 3.9 4.3 - - - +
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Residues in contact with PHE 892 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753K VAL* 3.6 43.5 - - + -
754K ARG 3.8 8.3 - - - -
755K ALA* 4.8 6.1 - - + -
806K LYS* 4.7 0.9 - - - -
834K ASN* 3.7 32.1 - - + +
835K ILE* 2.9 33.0 + - - +
836K LEU* 4.5 14.8 - - + -
837K VAL* 3.6 5.5 - - - +
873K PHE* 4.6 7.6 - + - -
876K ALA* 4.8 9.6 - - + -
877K THR* 4.9 10.5 - - + -
887K LEU* 5.1 3.6 - - + -
890K VAL* 4.6 3.4 - - + -
891K CYS* 1.3 74.2 - - - +
893K VAL* 1.3 79.9 + - - +
969K CYS* 3.9 20.4 - - + -
973K LEU* 4.2 29.2 - - + -
976K LYS* 5.1 0.7 - - - -
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Residues in contact with VAL 893 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753K VAL* 3.3 7.4 - - - +
754K ARG* 2.8 77.4 + - + +
756K MET* 4.5 4.7 - - + -
806K LYS* 3.5 29.8 - - + -
835K ILE 4.6 0.2 - - - -
837K VAL* 3.7 17.7 - - + -
839K LYS* 4.2 13.9 - - - +
891K CYS 3.9 6.5 - - - +
892K PHE* 1.3 86.9 - - - +
894K LEU* 1.3 70.0 + - - +
895K GLU* 4.0 2.9 + - - +
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Residues in contact with LEU 894 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751K LEU* 4.6 2.9 - - + -
752K SER 3.7 2.7 - - - +
753K VAL* 3.7 16.2 - - + -
824K TRP* 5.3 3.8 - - + -
836K LEU* 4.7 17.5 - - + +
837K VAL* 3.9 26.4 - - - +
839K LYS* 3.6 14.6 - - - +
847K VAL* 4.2 31.7 - - + +
869K ILE* 5.7 1.6 - - + -
873K PHE* 3.5 39.5 - - + -
892K PHE* 4.8 0.2 - - - -
893K VAL* 1.3 75.6 - - - +
895K GLU* 1.3 66.5 + - - +
896K LYS* 3.5 28.3 - - - +
897K TRP* 4.4 3.1 - - + +
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Residues in contact with GLU 895 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704K MET 4.1 14.8 - - - +
705K VAL* 3.6 29.1 - - + +
706K ASN* 4.0 6.6 + - - +
707K GLU* 3.7 25.3 + - - +
752K SER* 3.1 23.0 + - - +
753K VAL* 4.4 1.1 - - - +
754K ARG* 5.3 1.5 + - + +
839K LYS* 3.5 37.4 + - - +
843K PHE* 4.1 7.6 - - - -
893K VAL* 4.0 6.4 + - - +
894K LEU* 1.3 74.4 - - - +
896K LYS* 1.3 72.8 + - + +
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Residues in contact with LYS 896 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704K MET* 4.3 26.7 - - - +
750K THR* 4.5 14.5 + - - -
751K LEU* 3.4 25.5 - - - +
752K SER* 3.5 21.7 + - - +
843K PHE* 4.3 15.0 - - + -
894K LEU* 3.5 10.8 - - - +
895K GLU* 1.3 91.3 - - + +
897K TRP* 1.3 60.3 + - - +
898K ASP* 3.6 27.4 + - - +
901K LYS* 5.5 2.8 - - - +
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Residues in contact with TRP 897 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749K ALA* 4.7 11.5 - - - +
750K THR 3.5 15.3 - - - -
751K LEU* 4.1 19.6 - - + +
843K PHE* 3.7 6.3 - - - -
846K SER* 3.1 49.1 - - - -
847K VAL* 3.8 17.4 - - + +
865K LEU* 3.9 27.1 - - + -
868K SER* 4.1 10.1 - - - -
869K ILE* 3.3 36.6 - - + -
873K PHE* 5.1 3.6 - + + -
894K LEU* 4.5 10.1 - - + -
896K LYS* 1.3 74.3 - - - +
898K ASP* 1.3 79.4 + - - +
899K LEU* 4.6 12.1 - - + -
961K LEU* 4.6 18.6 - - + +
964K THR* 5.6 2.2 - - - +
965K MET* 3.4 28.1 - - + +
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Residues in contact with ASP 898 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749K ALA* 3.8 13.7 - - - -
750K THR 3.7 7.7 + - - +
843K PHE* 3.6 24.4 - - - +
844K GLN* 3.6 25.9 - - - +
896K LYS* 3.6 28.4 + - - +
897K TRP* 1.3 91.5 + - - +
899K LEU* 1.3 59.4 + - - +
901K LYS* 3.4 41.5 + - + +
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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