Contacts of the strand formed by residues 1024 - 1029 (chain N) in PDB entry 3O3U
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 GLN1024 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023N ALA* 1.3 72.1 - - - +
1025N ASN* 1.3 70.8 + - - +
1026N ILE* 3.4 22.5 + - + +
1039N LYS* 5.2 4.2 + - - -
1112N ASN 2.8 16.4 + - - +
1113N TYR* 3.4 23.1 + - + -
1114N ARG 2.9 21.8 + - - -
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Residues in contact with ASN1025 (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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1023N ALA 3.5 7.0 + - - -
1024N GLN* 1.3 76.7 + - - +
1026N ILE* 1.3 66.6 + - - +
1027N THR* 4.4 5.1 + - + -
1114N ARG* 2.9 48.5 + - - +
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Residues in contact with ILE1026 (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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1024N GLN* 3.8 26.5 - - + +
1025N ASN* 1.3 81.4 - - - +
1027N THR* 1.3 71.4 + - - +
1034N LEU* 3.7 39.0 - - + -
1036N LEU* 4.1 10.1 - - + -
1113N TYR* 3.7 32.3 - - + -
1114N ARG 2.9 10.0 + - - +
1115N VAL* 4.1 7.4 - - + -
1116N ARG* 3.0 26.2 + - - +
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Residues in contact with THR1027 (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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1025N ASN* 4.4 5.1 + - + +
1026N ILE* 1.3 88.0 - - - +
1028N ALA* 1.3 62.2 + - - +
1034N LEU* 4.9 1.9 - - - +
1116N ARG* 3.2 9.0 - - + +
1118N TYR* 4.6 7.6 - - - -
1216N ARG* 3.6 48.9 - - + +
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Residues in contact with ALA1028 (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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1027N THR* 1.3 77.8 - - - +
1029N ARG* 1.3 59.7 + - - +
1032N GLU* 6.0 0.7 - - + -
1033N PRO 5.1 4.0 - - - +
1034N LEU* 4.3 29.6 - - + -
1089N VAL* 3.9 20.4 - - + -
1115N VAL* 5.4 0.2 - - + -
1116N ARG 3.1 8.0 + - - +
1117N VAL* 3.0 30.4 - - + +
1118N TYR* 3.1 10.0 + - - -
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Residues in contact with ARG1029 (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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1028N ALA* 1.3 72.4 - - - +
1030N ILE* 1.3 74.7 + - - +
1031N GLY 3.2 0.2 + - - -
1032N GLU* 3.0 56.3 + - - +
1089N VAL* 3.2 8.2 - - - +
1118N TYR* 3.3 38.7 + - + +
1119N GLN* 2.8 30.5 + - - +
1120N ILE* 3.7 31.7 + - - +
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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