Contacts of the helix formed by residues 69 - 75 (chain I) in PDB entry 5IYB
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 ILE 69 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ILE 3.4 25.1 - - - +
608B ARG* 4.9 10.3 - - + +
610B ARG* 3.5 52.7 - - + +
67I GLN* 2.7 20.4 + - - +
68I ILE* 1.3 72.2 - - + +
70I ALA* 1.3 66.1 + - - +
71I ASP* 3.1 26.7 + - + +
72I VAL* 3.1 28.3 + - + +
122I ARG* 5.8 0.7 - - - +
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Residues in contact with ALA 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I ILE 3.6 3.1 + - - -
69I ILE* 1.3 67.6 - - - +
71I ASP* 1.3 61.6 + - - +
72I VAL* 3.0 10.7 + - - +
73I SER* 2.9 26.9 + - - -
113I VAL* 4.2 6.0 - - + +
120I GLY* 3.6 34.9 - - - +
122I ARG* 5.3 9.8 - - - +
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Residues in contact with ASP 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B PRO* 5.4 6.8 - - - +
605B ARG* 4.2 13.1 + - - +
607B ILE* 3.2 19.0 - - + +
610B ARG* 4.6 10.5 - - + +
69I ILE* 3.1 17.1 + - + +
70I ALA* 1.3 79.3 - - - +
72I VAL* 1.3 62.7 + - - +
73I SER* 3.1 1.1 - - - -
74I GLN* 3.2 38.4 + - - +
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Residues in contact with VAL 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ILE* 3.9 11.0 - - + -
608B ARG* 4.1 24.5 - - + -
68I ILE* 4.1 12.3 - - + -
69I ILE* 3.1 24.2 + - + +
70I ALA* 3.9 4.7 - - - +
71I ASP* 1.3 77.3 - - - +
73I SER* 1.3 64.3 + - - +
74I GLN 3.1 1.6 + - - -
75I ASP* 3.1 21.0 + - + +
78I LEU* 3.8 24.3 - - + +
95I VAL* 5.1 0.2 - - - +
97I PHE* 3.9 14.6 - - + -
113I VAL* 4.0 26.9 - - + -
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Residues in contact with SER 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I ALA 2.9 17.3 + - - -
71I ASP* 3.1 2.6 - - - -
72I VAL* 1.3 78.1 - - - +
74I GLN* 1.3 64.8 + - - +
75I ASP 3.3 0.7 - - - -
80I ARG* 3.1 23.4 + - - -
95I VAL* 3.8 16.1 - - - +
113I VAL* 4.1 7.9 - - - -
114I CYS 4.1 7.2 + - - -
115I THR* 3.4 40.8 + - - -
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Residues in contact with GLN 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B GLU* 3.6 38.6 + - + +
605B ARG* 3.2 35.7 + - - +
607B ILE* 4.4 3.1 - - + +
71I ASP* 3.2 33.9 + - - +
72I VAL 3.1 0.6 + - - -
73I SER* 1.3 81.7 + - - +
75I ASP* 1.3 63.6 + - - +
76I PRO* 3.2 9.9 - - - +
80I ARG* 3.8 7.3 + - - +
115I THR* 5.2 1.6 - - - +
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Residues in contact with ASP 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A LYS* 3.3 23.4 + - - -
607B ILE* 4.0 20.2 - - + +
672B THR 5.0 0.5 - - - +
72I VAL* 3.1 17.5 + - + +
73I SER 3.3 0.9 - - - +
74I GLN* 1.3 74.5 - - - +
76I PRO* 1.3 72.5 - - - +
77I THR* 2.8 28.7 + - - +
78I LEU* 3.4 27.3 + - + +
80I ARG* 2.9 19.7 + - - -
95I VAL* 5.0 0.2 - - - +
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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
------------------------------------------------------------
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