Contacts of the strand formed by residues 69 - 75 (chain H) in PDB entry 1CBV
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 ARG 69 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 3.9 3.8 - - - +
65H SER 2.7 29.4 + - - -
66H VAL* 3.3 20.2 - - - +
67H LYS 2.7 13.2 + - - +
68H ASP* 1.3 75.9 - - - +
70H PHE* 1.3 74.9 - - + +
71H THR* 4.3 0.7 + - - -
84H GLN 3.8 1.2 - - - +
86H ASN* 3.1 40.5 + - - +
87H ASN* 3.0 33.0 - - + +
88H LEU* 4.1 0.2 - - - +
89H LYS* 3.6 27.9 - - - +
91H GLU* 5.2 3.8 + - - +
92H ASP* 2.7 36.0 + - - -
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Residues in contact with PHE 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H VAL* 3.9 11.0 - - + -
49H ALA* 5.9 0.4 - - + -
62H TYR* 3.6 26.8 - - + -
66H VAL* 2.9 46.3 + - + +
68H ASP* 4.5 7.2 + - - -
69H ARG* 1.3 109.5 - - + +
71H THR* 1.3 64.1 + - - +
83H LEU* 3.6 25.8 - - + -
84H GLN 3.0 8.1 - - - +
85H MET* 3.3 47.8 - - + -
86H ASN 4.4 0.2 - - - -
88H LEU* 4.2 4.7 - - + -
92H ASP* 4.1 10.8 - - - -
96H TYR* 3.5 15.3 - + - -
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Residues in contact with THR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H TYR* 3.5 7.4 - - - +
69H ARG 5.3 0.9 + - - -
70H PHE* 1.3 75.0 + - - +
72H ILE* 1.3 69.7 + - - +
73H SER* 4.1 9.9 + - - +
83H LEU* 3.2 9.0 + - - -
84H GLN* 2.7 51.9 + - + +
86H ASN* 5.5 1.2 + - - -
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H MET 3.7 9.6 - - - +
36H TRP* 3.6 20.6 - - + -
49H ALA* 4.3 5.6 - - + -
50H ARG* 3.6 26.2 - - - +
51H ILE* 3.6 35.5 - - + +
60H THR* 3.4 20.7 + - - +
62H TYR* 3.0 33.2 + - + +
71H THR* 1.3 75.5 - - - +
73H SER* 1.3 64.3 + - - +
81H LEU* 3.5 9.6 - - + -
82H TYR 3.5 14.8 - - - +
83H LEU* 4.6 1.3 - - + +
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Residues in contact with SER 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ILE* 4.2 4.3 - - - -
71H THR* 4.7 11.2 + - - +
72H ILE* 1.3 75.0 - - - +
74H ARG* 1.3 63.6 + - - +
81H LEU* 3.1 9.3 - - - +
82H TYR* 2.9 53.0 + - - +
84H GLN* 5.4 1.6 + - - +
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Residues in contact with ARG 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H PHE* 3.5 26.1 + - + -
30H ASN 4.9 0.2 + - - -
32H ASN 2.7 29.2 + - - -
34H MET* 3.4 24.8 - - - +
51H ILE* 3.3 25.7 + - + +
52H ARG 2.8 26.8 + - - -
53H SER* 4.3 6.0 - - - -
58H TYR* 3.1 39.6 - - + -
73H SER* 1.3 77.2 - - - +
75H ASP* 1.3 63.3 + - - +
76H ASP* 3.1 24.8 + - - +
80H MET 3.4 11.7 - - - +
81H LEU* 4.5 4.7 - - + +
82H TYR* 5.0 1.6 - - - -
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Residues in contact with ASP 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H ARG* 1.3 75.1 - - - +
76H ASP* 1.3 66.5 + - - +
77H SER* 2.9 29.1 + - - -
78H GLN* 3.0 31.7 + - - +
79H ASN 3.2 8.0 + - - -
80H MET* 2.9 21.5 + - + +
82H TYR* 4.2 19.9 + - + -
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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