Contacts of the strand formed by residues 83 - 93 (chain E) in PDB entry 2SGQ
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 THR 83 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E TRP* 3.2 5.8 - - - +
68E ALA* 2.8 48.1 + - + -
78E ASN* 2.9 15.7 + - - -
82E THR* 1.4 81.9 + - - +
84E VAL* 1.3 62.9 + - - +
110E ASN* 3.7 18.4 - - - +
113E ILE* 4.4 9.6 - - + -
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Residues in contact with VAL 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 4.6 10.8 - - + -
66E TRP 3.8 3.1 - - - +
67E TRP* 3.5 26.7 - - + +
82E THR 3.8 5.5 + - - +
83E THR* 1.3 78.1 - - - +
85E LEU* 1.3 63.9 + - - +
86E GLY* 3.9 5.2 - - - +
87E THR* 6.3 0.2 - - + -
109E THR* 3.8 21.1 - - - +
110E ASN* 2.8 31.6 + - + +
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.9 16.4 - - + -
31E ILE* 3.7 28.0 - - + -
44E LEU* 5.2 0.4 - - + -
52E PHE* 4.1 21.5 - - + -
66E TRP* 2.7 16.8 + - + +
67E TRP 3.7 17.7 - - - +
68E ALA* 3.5 18.6 - - + +
84E VAL* 1.3 75.3 - - - +
86E GLY* 1.3 57.8 + - - +
106E VAL* 5.3 0.4 - - - -
108E TYR* 3.5 27.6 - - + -
109E THR* 3.0 20.8 + - - -
110E ASN* 3.1 9.2 + - - +
113E ILE* 3.5 33.9 - - + -
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Residues in contact with GLY 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 3.7 3.1 - - - +
66E TRP* 3.1 25.6 + - - +
84E VAL* 3.9 2.1 - - - +
85E LEU* 1.3 82.8 - - - +
87E THR* 1.4 68.5 + - - +
106E VAL* 3.8 8.0 - - - +
107E ARG 3.2 12.8 - - - -
109E THR* 3.2 15.4 + - - -
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Residues in contact with THR 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E THR* 3.3 13.2 - - - +
65E THR* 4.1 17.0 - - + +
86E GLY* 1.4 79.2 - - - +
88E THR* 1.4 67.1 + - - +
89E SER* 3.3 3.6 + - - -
106E VAL* 3.7 4.5 - - - +
107E ARG* 2.8 47.4 + - - +
109E THR* 4.3 16.0 - - + +
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Residues in contact with THR 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E THR* 4.0 18.2 - - + +
63E ALA* 3.0 28.3 + - - +
64E THR* 2.9 10.0 + - - +
66E TRP* 3.0 22.9 + - - -
87E THR* 1.4 75.0 + - - +
89E SER* 1.3 62.2 + - - +
90E GLY* 3.8 22.9 - - - +
91E SER* 4.6 2.2 - - - -
105E ILE 3.7 6.5 - - - +
106E VAL* 4.1 5.7 - - - +
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Residues in contact with SER 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TYR* 4.1 14.0 - - - -
87E THR* 3.3 3.0 + - - -
88E THR* 1.3 72.6 + - - +
90E GLY* 1.4 58.4 + - - +
105E ILE* 2.9 20.7 + - - +
107E ARG* 3.4 31.0 + - - +
237E TYR* 5.7 0.2 - - - -
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Residues in contact with GLY 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E THR* 3.7 7.0 - - - +
89E SER* 1.4 82.5 - - - +
91E SER* 1.3 63.7 + - - -
104E GLY* 3.3 1.4 - - - -
105E ILE* 2.9 34.7 + - - +
237E TYR* 3.6 14.6 - - - -
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Residues in contact with SER 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E GLY 3.4 11.1 + - - -
59E THR* 2.9 32.0 + - - -
60E ASP* 3.5 13.9 + - - +
88E THR* 4.6 3.4 - - - -
90E GLY* 1.3 77.1 - - - -
93E SER* 1.3 62.5 + - - +
94E PHE 4.1 2.1 + - - -
103E TYR 3.8 2.5 - - - -
237E TYR* 3.7 3.3 + - - -
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Residues in contact with SER 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E SER* 1.3 75.0 + - - +
94E PHE* 1.3 59.1 + - - +
99E PRO 4.2 1.8 + - - -
101E ASN* 2.9 36.8 + - - +
103E TYR* 2.7 62.0 + - - +
237E TYR* 4.1 1.5 + - - -
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Residues in contact with PHE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E GLY* 3.6 20.2 - - - +
57E HIS* 3.7 28.5 - - + -
60E ASP* 4.4 22.2 - - + +
91E SER* 4.1 3.1 + - - +
93E SER* 1.3 75.5 - - - +
99E PRO* 1.3 74.2 + - + +
101E ASN 3.3 10.3 - - - -
102E ASP* 3.3 24.0 - - - -
171E TYR* 4.2 14.6 - + + -
175E ASP* 3.8 37.2 - - + -
177E VAL* 3.8 20.2 - - + -
17I THR* 4.2 5.8 - - + -
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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