Contacts of the strand formed by residues 1070 - 1073 (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 GLU1070 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002N THR* 3.4 25.7 - - + +
1004N GLU* 5.3 0.3 - - - +
1006N ILE* 4.0 4.0 - - - +
1033N LYS* 2.4 29.6 + - - +
1064N TYR* 4.1 18.5 - - + -
1065N GLN* 5.7 0.7 - - + +
1068N GLY 3.1 15.9 - - - +
1069N PHE* 1.3 72.9 - - - +
1071N VAL* 1.3 70.9 + - - +
1072N MET* 4.1 2.6 - - + +
1084N GLN* 3.3 2.9 - - - -
1085N ILE 3.0 31.0 + - - +
1087N PHE* 4.1 12.5 - - + +
201O TRP* 3.8 10.8 - - - -
44V TYR* 2.4 25.3 + - - -
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Residues in contact with VAL1071 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002N THR* 3.7 17.4 - - - -
1003N ALA* 4.5 2.6 + - + -
1070N GLU* 1.3 74.9 - - - +
1072N MET* 1.3 76.8 + - - +
1073N TYR* 4.3 14.8 - - + +
1080N LYS* 4.3 23.1 - - + -
1081N LEU 5.1 1.8 - - - +
1084N GLN* 4.5 11.4 - - + +
189O THR* 4.3 11.9 - - + +
191O TYR* 4.2 29.8 - - + +
201O TRP* 4.1 11.1 - - + -
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Residues in contact with MET1072 (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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826N ALA* 4.2 4.7 - - + -
828N ALA* 5.6 0.2 - - + -
1000N PRO* 4.5 16.4 - - + +
1001N PHE 3.0 17.7 - - - +
1002N THR* 3.8 21.8 - - + -
1070N GLU* 3.6 5.7 + - + +
1071N VAL* 1.3 87.5 - - - +
1073N TYR* 1.3 65.8 + - - +
1080N LYS* 3.6 2.1 - - - -
1081N LEU* 2.8 33.9 + - + +
1083N ALA 4.7 2.6 + - - -
1085N ILE* 2.9 69.0 - - + +
1087N PHE* 3.8 29.8 - - + -
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Residues in contact with TYR1073 (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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1000N PRO* 3.2 4.2 - - - +
1001N PHE* 2.6 71.1 + + + -
1003N ALA* 3.6 22.7 - - + +
1071N VAL* 4.3 13.5 - - + +
1072N MET* 1.3 78.6 - - - +
1074N ASN* 1.3 59.7 + - - +
1075N GLY 3.1 8.3 + - - -
1078N GLY 3.4 17.3 - - - +
1079N LYS 3.2 9.0 - - - +
1080N LYS* 3.1 39.3 - - + +
1081N LEU* 4.3 2.9 - - - -
178O PHE* 3.8 12.1 - + - -
179O GLU* 3.2 30.3 - - - +
180O TYR* 3.5 19.2 + + - -
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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