Contacts of the strand formed by residues 68 - 75 (chain A) in PDB entry 2G8I
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 LEU 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A SER* 1.3 75.4 - - - +
69A SER* 1.3 54.4 + - - +
70A VAL* 4.1 9.0 - - + -
85A GLY* 4.1 4.7 - - - -
86A VAL 3.5 26.9 - - - +
87A ASP* 5.2 0.2 - - - +
88A THR* 3.7 1.8 - - - -
94A LEU* 3.7 22.9 - - + -
95A PHE* 3.9 15.0 - - + -
116A GLY* 3.7 36.1 - - - +
119A TYR* 4.3 4.3 - - + -
120A LEU* 3.9 25.8 - - + -
127A LYS* 4.7 1.0 - - + +
128A PRO 3.0 10.1 + - - +
129A ILE* 3.2 11.3 - - + +
130A TYR* 2.7 31.7 + - - +
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 1.3 73.6 - - - +
70A VAL* 1.3 61.5 + - - +
85A GLY* 3.3 2.1 - - - -
86A VAL* 2.8 51.4 + - - -
88A THR* 2.6 30.0 + - - +
130A TYR* 3.6 16.4 - - - +
181A TRP* 4.6 1.9 - - - -
189A ILE* 4.0 21.0 - - - +
190A LYS* 4.5 6.0 - - - +
191A ALA* 3.5 5.1 - - - +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 4.1 14.6 - - + -
69A SER* 1.3 78.5 - - - +
71A ASP* 1.3 67.7 + - - +
84A LYS 3.3 8.1 - - - +
85A GLY* 4.0 0.7 - - - -
95A PHE* 3.8 21.5 - - + -
109A GLU* 4.9 0.8 - - - +
112A ALA* 3.6 29.8 - - + +
113A ILE* 3.9 27.8 - - + -
116A GLY* 4.6 0.7 - - - -
129A ILE* 4.1 9.9 - - + -
130A TYR 3.0 14.2 + - - +
131A SER* 4.1 7.3 + - - +
132A ASP 4.8 0.3 + - - -
189A ILE* 3.3 16.1 - - - +
191A ALA* 3.7 1.8 - - - -
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 1.3 78.9 - - - +
72A VAL* 1.3 63.7 + - - +
83A TYR* 3.3 5.7 - - - +
84A LYS 3.2 29.3 + - - +
109A GLU* 3.0 9.4 - - - +
112A ALA* 4.4 3.4 - - - -
132A ASP* 3.4 2.4 - - - +
189A ILE* 3.6 12.0 - - + +
191A ALA* 3.5 21.1 - - + +
192A ASN* 3.2 11.6 - - - -
193A TYR* 3.6 4.1 - - - -
401A MN 2.1 34.3 + - - -
402A MN 2.2 30.1 + - - -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP* 1.3 87.5 + - - +
73A GLY* 1.3 71.2 + - - +
74A SER* 5.2 1.8 - - - +
81A VAL* 3.6 11.7 - - + -
82A GLU 3.1 16.4 - - - +
83A TYR* 4.1 2.2 - - - -
105A ASN* 3.8 18.2 - - + +
108A GLY* 3.6 23.8 - - - -
109A GLU* 3.2 43.8 + - + +
193A TYR* 3.3 12.3 - - - +
401A MN 4.3 2.0 - - - +
402A MN 4.0 4.7 + - - -
6B A 5.0 1.8 - - + +
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 1.3 78.5 - - - +
74A SER* 1.3 62.6 + - - -
81A VAL* 3.6 0.9 - - - -
82A GLU* 2.9 42.0 + - - +
193A TYR* 3.4 29.0 - - - -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 5.2 4.0 - - - +
73A GLY* 1.3 75.1 - - - -
75A GLN* 1.3 60.1 + - - +
76A GLY 2.9 22.6 + - - -
77A ASN* 4.6 5.3 - - - +
80A ILE 3.0 15.5 - - - -
81A VAL* 4.3 10.5 - - - -
82A GLU* 5.5 0.4 - - - -
105A ASN* 5.5 8.8 - - - +
193A TYR* 5.4 0.4 - - - +
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A SER* 1.3 72.9 - - - +
76A GLY* 1.3 59.3 + - - +
79A GLY* 3.4 2.8 - - - -
80A ILE* 3.0 56.8 + - + +
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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