Contacts of the strand formed by residues 1023 - 1030 (chain N) in PDB entry 6VEN
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 CYS1023 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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964N ILE* 3.6 18.2 - - - -
1015N ILE* 6.1 0.7 - - + -
1021N PRO* 3.6 8.8 - - - +
1022N ASN* 1.3 99.1 - - - +
1024N THR* 1.3 65.0 + - - +
1038N ILE* 3.8 16.4 - - + -
1039N TYR 3.2 11.4 - - - +
1041N LEU 3.8 1.3 - - - +
1044N ILE* 3.6 16.8 - - - -
1050N LEU* 3.8 14.4 - - - -
1051N THR 3.2 10.8 + - - +
1052N TYR* 3.5 26.9 - - + -
1053N ASP* 4.2 0.3 + - - +
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Residues in contact with THR1024 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021N PRO* 5.8 2.5 - - + -
1023N CYS* 1.3 80.0 - - - +
1025N ALA* 1.3 62.8 + - - +
1026N LYS* 4.5 14.9 - - - +
1038N ILE* 3.2 8.1 - - - +
1039N TYR* 2.9 41.2 + - - +
1041N LEU* 3.6 39.9 - - + -
1052N TYR* 4.3 7.4 - - - -
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Residues in contact with ALA1025 (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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6A THR* 3.2 29.9 - - + +
995N PHE* 4.2 7.4 - - + -
1024N THR* 1.3 76.9 - - - +
1026N LYS* 1.3 62.3 + - - +
1036N ILE* 4.3 6.3 - - + -
1037N VAL 3.2 8.5 - - - +
1038N ILE* 4.4 5.8 - - + -
1052N TYR* 3.5 33.8 - - + +
1055N LYS* 5.5 2.6 + - - -
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Residues in contact with LYS1026 (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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6A THR* 5.6 0.2 - - - -
72G ASP 5.1 7.8 + - - +
74G LYS* 4.3 29.3 - - - +
961N LYS* 5.9 7.5 - - - +
1024N THR* 4.2 11.4 + - - +
1025N ALA* 1.3 77.5 - - - +
1027N ILE* 1.3 65.2 + - - +
1028N ILE* 3.9 6.3 - - + -
1036N ILE* 3.5 5.5 - - - +
1037N VAL* 2.9 32.8 + - + +
1039N TYR* 3.5 42.8 - - + +
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Residues in contact with ILE1027 (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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6A THR* 3.3 34.5 - - + +
74G LYS* 5.2 8.8 - - - +
996N ARG 4.6 4.0 - - - +
997N VAL* 3.5 28.5 - - + +
1026N LYS* 1.3 79.1 - - - +
1028N ILE* 1.3 67.9 + - - +
1029N LYS* 5.4 3.6 - - - +
1034N ARG* 3.9 34.8 - - + +
1035N ARG 3.2 13.9 - - - +
1036N ILE* 4.7 8.5 - - + -
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Residues in contact with ILE1028 (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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71G ARG* 3.9 40.8 - - + +
72G ASP* 5.1 1.3 - - - -
74G LYS* 4.9 19.1 - - + -
934N ASN* 5.8 1.8 - - - +
936N ARG* 5.9 1.1 - - - +
1026N LYS* 3.9 5.3 - - + -
1027N ILE* 1.3 80.6 - - - +
1029N LYS* 1.3 72.8 + - - +
1030N VAL* 4.0 15.7 - - + -
1034N ARG* 3.3 4.7 - - - -
1035N ARG* 2.8 35.0 + - + +
1037N VAL* 3.5 31.6 - - + -
1039N TYR* 3.5 23.1 - - + +
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Residues in contact with LYS1029 (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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71G ARG* 4.8 3.6 + - - -
1027N ILE* 5.4 3.4 - - - +
1028N ILE* 1.3 80.6 - - + +
1030N VAL* 1.3 65.4 + - - +
1032N GLY* 4.6 9.6 + - - +
1033N ARG 3.1 19.1 - - - +
1034N ARG* 4.3 32.9 - - + +
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Residues in contact with VAL1030 (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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71G ARG* 3.6 37.5 - - - +
51H ASP* 3.8 18.8 - - - +
933N LEU* 4.2 17.0 - - + -
934N ASN* 4.2 13.5 - - - +
1028N ILE* 4.0 11.8 - - + -
1029N LYS* 1.3 75.8 - - - +
1031N GLY* 1.3 61.2 + - - +
1032N GLY 3.0 4.5 - - - -
1033N ARG* 2.9 27.0 + - - +
1035N ARG* 4.2 32.9 + - + +
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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