Contacts of the strand formed by residues 70 - 75 (chain H) in PDB entry 3Q3G
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 ALA 70 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ILE* 3.4 33.0 - - + -
62H TYR* 3.3 21.6 - - + -
66H PHE* 2.9 18.8 + - + +
67H GLN* 5.6 1.6 + - - -
68H GLY 4.9 4.0 + - - -
69H LYS* 1.3 76.5 + - - +
71H THR* 1.3 65.0 + - - +
83H LEU* 3.7 12.1 - - + -
84H GLN 3.3 4.3 - - - -
85H LEU* 4.2 7.4 - - + -
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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
----------------------------------------------------------
21H LYS* 5.9 0.3 - - - -
62H TYR* 3.5 8.3 - - - +
68H GLY 5.6 1.6 + - - -
69H LYS 4.9 1.9 + - - -
70H ALA* 1.3 76.8 + - - +
72H ILE* 1.3 62.5 - - - +
73H THR* 4.0 19.1 + - + +
82H TYR* 3.9 0.9 - - - +
83H LEU* 3.6 1.2 - - - -
84H GLN* 2.8 57.0 + - + +
86H SER* 5.6 1.0 + - - -
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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
----------------------------------------------------------
38H TRP* 3.6 30.7 - - + +
50H ILE* 4.3 4.0 - - + -
51H GLY* 3.4 43.1 - - - +
52H ARG 3.7 2.5 - - - +
53H ILE* 3.6 31.5 - - + +
60H THR* 3.4 23.8 - - + +
61H LYS 4.8 0.2 - - - +
62H TYR* 2.9 30.3 + - + +
71H THR* 1.3 74.8 - - - +
73H THR* 1.3 65.4 + - - +
82H TYR 3.3 13.5 - - - +
83H LEU* 3.9 11.4 - - + -
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Residues in contact with THR 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LYS* 4.0 12.8 + - - +
53H ILE* 3.6 9.1 - - - +
71H THR* 4.4 17.9 + - + +
72H ILE* 1.3 80.6 - - - +
74H ALA* 1.3 60.5 + - - +
81H ALA* 3.5 4.0 - - - +
82H TYR* 2.7 54.1 + - - +
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Residues in contact with ALA 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ILE* 3.9 7.2 - - + -
53H ILE* 3.6 18.8 - - + +
55H PRO* 3.7 33.9 - - + +
58H ASP* 3.9 19.2 + - - +
73H THR* 1.3 77.6 - - - +
75H ASP* 1.3 59.7 + - - +
76H THR* 4.0 1.8 + - - +
80H THR 3.5 5.2 - - - +
81H ALA* 4.2 2.2 - - - +
82H TYR* 4.5 2.7 - - - -
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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
----------------------------------------------------------
31H ILE* 3.8 1.8 - - - -
74H ALA* 1.3 71.7 - - - +
76H THR* 1.3 60.2 + - - +
77H SER* 3.4 21.9 + - - -
78H SER* 2.6 29.9 + - - +
79H ASN* 2.9 22.0 + - - -
80H THR 2.7 18.3 + - - -
82H TYR* 3.6 22.6 + - + -
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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