Contacts of the strand formed by residues 821 - 827 (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 GLN 821 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796N LEU* 3.3 29.4 - - + +
798N TYR* 3.4 26.1 + - - +
800N GLN* 3.9 15.0 - - + +
820N GLY* 1.3 77.5 - - - +
822N ASN* 1.3 64.4 + - - +
823N ALA* 3.4 2.1 + - - -
849N GLY 5.4 0.2 + - - -
850N LEU* 2.8 32.7 - - + +
851N PHE* 3.1 40.7 + - + +
852N ARG 4.8 0.4 + - - +
1091N TYR* 3.6 8.0 - - - -
1092N TYR* 2.9 32.9 + - - +
8V PHE* 3.4 11.6 - - + -
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Residues in contact with ASN 822 (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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800N GLN* 2.8 28.0 + - - +
801N LYS 2.7 28.9 + - - -
803N LEU* 3.0 44.5 + - + +
821N GLN* 1.3 69.6 - - - +
823N ALA* 1.3 60.7 + - - +
850N LEU* 6.0 0.3 - - - +
1028N GLU* 5.4 0.2 - - - +
1032N SER* 5.0 0.3 + - - -
1089N PRO* 4.7 4.5 - - + -
1090N THR 3.9 6.2 - - - -
1091N TYR* 3.5 19.6 + - - +
8V PHE* 5.8 1.4 - - - -
48V ARG* 3.1 34.6 + - - -
52V THR* 3.2 11.5 + - - +
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Residues in contact with ALA 823 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821N GLN 3.4 5.0 + - - +
822N ASN* 1.3 74.7 - - - +
824N ILE* 1.3 67.3 + - - +
825N VAL* 3.0 9.6 + - + +
850N LEU* 4.9 4.9 - - + -
851N PHE* 4.7 11.4 - - + -
1009N ASP* 3.6 11.4 - - + +
1010N LEU* 3.5 31.9 - - + -
1089N PRO* 4.1 0.2 - - - -
1090N THR 3.1 29.1 + - - +
1092N TYR* 4.9 3.1 - - + -
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Residues in contact with ILE 824 (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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823N ALA* 1.3 68.6 - - - +
825N VAL* 1.3 58.2 + - - +
1006N ILE* 5.1 2.5 - - + -
1007N VAL 3.8 11.9 - - - +
1008N PRO* 3.5 1.9 - - - +
1009N ASP* 2.6 39.0 + - - +
1010N LEU 3.3 4.5 + - - -
1087N PHE* 3.6 38.8 - - + -
1088N GLY 4.0 6.5 - - - +
1089N PRO* 3.8 25.1 - - + -
9V SER* 3.6 9.9 - - - +
44V TYR* 4.0 22.0 - - + -
45V CYS* 4.3 9.2 - - + -
48V ARG* 2.8 35.9 - - + +
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Residues in contact with VAL 825 (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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823N ALA* 3.0 17.7 + - + +
824N ILE* 1.3 73.5 - - - +
826N ALA* 1.3 75.5 + - - +
827N ILE* 4.5 4.3 - - + +
1010N LEU* 3.8 13.9 - - + +
1012N ILE* 4.1 28.3 - - + -
1025N HIS* 5.3 2.0 - - + -
1029N CYS* 5.2 1.8 - - - -
1086N PHE* 3.9 1.7 - - - +
1087N PHE* 3.5 7.1 - - - -
1088N GLY 3.0 32.8 + - - +
1090N THR* 4.0 13.2 - - - +
1092N TYR* 3.6 31.4 - - + -
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Residues in contact with ALA 826 (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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825N VAL* 1.3 79.1 - - - +
827N ILE* 1.3 62.9 + - - +
828N ALA* 3.7 2.9 - - + +
1000N PRO* 5.6 2.5 - - + -
1008N PRO* 3.7 15.5 - - + +
1010N LEU 3.1 7.6 + - - +
1011N ILE* 3.2 10.7 - - + -
1012N ILE 2.8 24.4 + - - +
1072N MET* 4.2 11.9 - - + -
1085N ILE* 4.3 2.2 - - + -
1086N PHE 3.6 5.4 - - - -
1087N PHE* 3.5 23.1 - - + -
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Residues in contact with ILE 827 (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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663M SER* 2.4 35.3 + - - +
664M THR* 3.7 21.1 - - + +
825N VAL* 4.5 4.9 - - + +
826N ALA* 1.3 74.1 - - - +
828N ALA* 1.3 57.2 + - - +
1012N ILE* 3.1 32.8 - - + +
1013N ASN 4.1 1.6 - - - +
1014N PRO* 3.4 33.2 - - + -
1017N ILE* 4.8 7.2 - - + -
1025N HIS* 4.6 7.9 - - + +
1026N LEU* 4.0 16.2 - - + -
1085N ILE* 3.4 1.4 - - - +
1086N PHE* 3.2 38.5 + - + +
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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
------------------------------------------------------------
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