Contacts of the strand formed by residues 853 - 862 (chain N) in PDB entry 3HOU
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 853 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778N MET* 3.7 26.1 - - - -
795N ILE 3.3 14.4 - - - -
796N LEU* 4.1 3.4 - - - -
797N TYR* 3.8 9.4 - - - -
852N ARG* 1.3 79.9 - - - +
854N LEU* 1.3 63.2 + - - +
971N THR* 3.3 6.8 - - - +
972N LYS* 2.9 33.5 + - - +
1094N ARG* 2.5 30.1 + - - -
1098N MET* 5.4 0.3 - - - -
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Residues in contact with LEU 854 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785N TYR* 4.3 16.4 - - + +
793N ALA 4.4 0.2 - - - -
794N ASN* 3.5 7.3 - - - +
795N ILE* 2.7 41.0 + - + +
797N TYR* 3.0 36.1 - - + +
853N SER* 1.3 77.3 + - - +
855N PHE* 1.3 64.2 + - - +
856N PHE* 3.5 32.8 - - + -
969N ARG* 4.5 5.8 - - + -
970N THR 3.4 4.3 - - - +
971N THR* 3.3 14.8 - - - +
972N LYS* 5.9 0.2 - - - -
59O ALA* 4.7 15.0 - - + +
61O GLU* 4.2 9.6 - - + +
62O PHE* 4.9 11.7 - - + -
1V MET* 6.4 0.2 - - + -
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Residues in contact with PHE 855 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792N MET* 3.6 18.4 - - + -
793N ALA 3.2 8.5 - - - -
794N ASN* 3.4 21.3 - - - +
854N LEU* 1.3 79.3 - - - +
856N PHE* 1.3 75.3 + - - +
857N ARG* 3.1 37.7 - - + -
945N GLU* 4.2 19.3 - - + -
968N VAL 3.9 1.0 - - - +
969N ARG* 3.4 1.6 - - - -
970N THR* 2.8 49.8 + - - +
972N LYS* 3.4 44.4 - - + -
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Residues in contact with PHE 856 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785N TYR* 4.1 25.4 - + - -
786N ASN* 5.6 1.6 - - - -
790N ASP* 5.1 3.8 - - - +
792N MET* 3.0 4.8 - - - -
793N ALA* 2.8 47.0 + - + +
795N ILE* 4.7 9.4 - - + -
854N LEU* 3.5 41.5 - - + -
855N PHE* 1.3 83.6 - - - +
857N ARG* 1.3 60.2 + - - +
950N ASP* 3.4 20.4 - - - -
967N ARG* 3.3 40.2 - - + -
968N VAL 3.5 4.9 - - - -
969N ARG* 3.7 21.8 - - + -
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Residues in contact with ARG 857 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244 G 4.2 0.2 + - - -
791N THR* 5.2 1.8 - - - -
792N MET* 2.9 38.6 - - + +
855N PHE* 3.1 28.0 - - + -
856N PHE* 1.3 74.5 - - - +
858N SER* 1.3 68.2 + - - +
859N TYR* 3.6 32.5 + - + -
942N ARG* 2.8 50.9 - - - +
945N GLU* 2.7 39.6 + - - +
966N VAL 3.8 0.3 - - - +
967N ARG* 3.3 4.0 - - - +
968N VAL* 3.1 33.6 + - + +
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Residues in contact with SER 858 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789N MET* 3.3 32.3 + - - +
790N ASP 3.2 15.2 + - - -
791N THR* 3.4 22.9 - - - +
792N MET 3.8 7.3 - - - +
857N ARG* 1.3 82.4 + - - +
859N TYR* 1.3 65.5 + - - +
860N MET* 4.0 2.6 + - - +
965N LYS* 5.4 2.9 - - - -
966N VAL 3.2 8.3 - - - -
967N ARG* 3.7 18.6 - - - +
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Residues in contact with TYR 859 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857N ARG* 3.6 32.3 - - + -
858N SER* 1.3 76.4 - - - +
860N MET* 1.3 63.1 + - - +
911N ILE* 3.8 13.9 - - + -
912N ILE* 5.2 4.9 - - + -
939N THR* 4.7 19.1 - - + -
940N PRO 4.0 8.3 - - - -
941N LEU* 2.8 43.0 - - + +
942N ARG* 2.9 41.0 + - + +
945N GLU* 3.7 2.8 + - - -
965N LYS* 3.4 3.6 - - - +
966N VAL* 3.0 38.9 + - + +
968N VAL* 3.8 11.7 - - + -
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Residues in contact with MET 860 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121N ASN* 3.6 19.1 - - - +
858N SER 4.0 2.9 + - - +
859N TYR* 1.3 79.3 - - - +
861N ASP* 1.3 93.1 + - - +
862N GLN* 4.6 4.7 - - - +
912N ILE* 4.6 5.5 - - - +
939N THR* 5.0 7.5 - - - +
963N PHE* 3.6 21.5 - - + -
964N VAL 3.4 14.4 - - - +
965N LYS* 3.4 23.3 - - + +
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Residues in contact with ASP 861 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860N MET* 1.3 87.4 - - - +
862N GLN* 1.3 96.5 + - - +
874N PHE* 3.9 10.2 - - + -
912N ILE* 4.3 16.4 - - + -
914N LYS* 2.8 30.4 + - - +
937N ALA 4.4 2.4 - - - +
938N SER 5.3 0.2 - - - +
939N THR* 4.3 13.2 + - - +
963N PHE* 3.7 0.7 - - - -
964N VAL* 2.9 35.7 + - - +
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Residues in contact with GLN 862 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121N ASN* 5.5 2.3 - - - +
860N MET* 4.6 4.8 - - - +
861N ASP* 1.3 101.6 + - - +
863N GLU* 1.3 67.2 + - - +
864N LYS* 3.9 0.4 - - - +
872N GLU* 3.3 0.9 - - - +
874N PHE* 4.1 2.7 - - - -
914N LYS* 3.0 17.0 + - - -
957N ASN* 3.9 26.5 + - - +
959N ASP* 5.7 0.6 + - - -
961N LEU* 5.5 4.4 - - - +
962N LYS 3.1 11.4 - - - +
963N PHE* 3.0 44.5 - - + -
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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