Contacts of the strand formed by residues 80 - 85 (chain H) in PDB entry 4R2G
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 ASP 80 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ASN* 3.7 19.7 + - - +
31H SER* 2.9 36.4 + - - -
32H ASN* 4.7 2.3 + - - +
77H GLU 5.1 2.0 - - - +
78H ASP 3.1 11.0 + - - +
79H SER* 1.3 75.3 - - - +
81H THR* 1.3 82.1 + - - +
82H TYR* 3.6 19.4 - - + +
94H GLN* 3.8 3.9 - - - -
95H LEU 3.1 27.8 + - - +
96H LEU* 5.5 0.4 - - - +
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Residues in contact with THR 81 (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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30H ASN 3.0 1.7 - - - -
31H SER* 2.5 45.4 + - - -
80H ASP* 1.3 87.3 + - - +
82H TYR* 1.3 60.7 + - - +
83H ILE* 3.6 9.0 - - + +
92H GLU* 3.3 34.3 - - + +
93H VAL 3.2 9.0 - - - +
94H GLN* 4.0 19.1 - - - +
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Residues in contact with TYR 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 4.1 16.6 - - + -
28H TRP* 3.9 21.1 - - + -
29H LYS 3.2 13.9 - - - +
30H ASN* 4.1 10.3 - - + -
36H ILE* 3.5 32.8 - - + -
51H LEU* 3.3 20.1 - - + +
69H LEU* 4.1 9.6 - - + -
71H ILE* 4.5 5.5 - - + +
78H ASP* 2.4 33.8 + - - +
80H ASP* 3.6 27.4 - - + +
81H THR* 1.3 72.5 - - - +
83H ILE* 1.3 61.6 + - - +
91H GLU 3.8 0.5 - - - +
92H GLU* 3.5 2.8 - - - +
93H VAL* 2.9 37.8 + - + +
95H LEU* 4.3 15.0 - - + -
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Residues in contact with ILE 83 (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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27H HIS 3.5 1.4 - - - +
28H TRP* 3.2 10.0 - - - -
29H LYS* 2.8 34.0 + - + +
30H ASN 3.4 25.1 - - - +
31H SER* 4.2 4.3 - - - +
33H GLN* 4.5 9.0 - - - +
81H THR* 3.6 20.4 - - + +
82H TYR* 1.3 76.3 - - - +
84H CYS* 1.3 67.0 + - - +
85H GLU* 4.0 5.8 - - + +
90H LYS* 3.7 39.0 - - + +
91H GLU 3.2 9.6 - - - +
92H GLU* 3.6 23.8 - - + +
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Residues in contact with CYS 84 (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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15H THR 5.5 0.2 - - - +
16H CYS* 2.0 54.7 - - + -
26H PHE* 4.9 7.9 - - - -
27H HIS 3.9 2.5 - - - -
28H TRP* 3.9 28.2 - - + -
67H PHE 4.7 0.2 - - - -
83H ILE* 1.3 73.6 - - - +
85H GLU* 1.3 59.3 + - - +
86H VAL* 3.3 12.6 + - - +
89H GLN 3.1 12.9 - - - +
91H GLU* 2.9 27.8 + - + +
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Residues in contact with GLU 85 (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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25H GLN 3.9 1.6 - - - +
26H PHE* 3.4 19.6 - - - -
27H HIS* 3.1 24.9 + - + +
29H LYS* 3.1 39.8 + - + -
83H ILE* 4.8 5.8 - - + -
84H CYS* 1.3 68.2 - - - +
86H VAL* 1.3 59.0 + - - +
88H ASP 5.4 0.7 - - - -
89H GLN 3.4 7.4 - - - +
90H LYS* 3.4 42.6 + - + +
279K ASP* 4.0 6.7 - - - +
281K ALA* 3.4 16.1 - - - +
511K NAG 3.8 4.9 - - - +
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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