Contacts of the strand formed by residues 63 - 68 (chain A) in PDB entry 1G82
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 ARG 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A HIS* 4.4 9.1 + - - -
59A GLY 3.8 7.4 + - - +
60A ILE* 3.1 52.6 + - + +
62A ARG* 1.3 78.5 - - - +
64A ARG* 1.3 81.6 + - - +
94A ILE* 4.2 11.9 - - - +
95A LEU 3.2 8.7 - - - +
96A GLU* 5.1 3.7 - - - +
110A VAL* 3.5 40.5 - - - +
191A PRO* 4.7 0.3 - - - +
192A VAL* 4.2 26.3 + - + +
196A LYS 5.3 0.8 + - - -
197A VAL* 3.7 23.7 - - + +
198A PRO* 5.6 0.4 - - - +
199A GLU* 3.0 30.9 + - - +
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Residues in contact with ARG 64 (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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61A LEU 3.2 22.8 + - - -
62A ARG* 3.3 18.3 - - - +
63A ARG* 1.3 104.4 + - - +
65A GLN* 1.3 66.4 + - - +
93A GLY 3.6 0.9 - - - +
94A ILE* 3.7 1.0 - - - -
95A LEU* 2.8 35.1 + - - +
97A PHE* 3.5 42.3 - - + +
189A PRO* 4.4 8.8 - - + +
190A ARG 3.3 9.9 - - - +
191A PRO* 5.6 0.2 - - - +
192A VAL* 3.9 4.8 - - - +
191D PRO* 3.4 37.7 - - - +
192D VAL 3.3 26.9 + - - -
193D ASP* 4.2 9.7 - - - +
194D PRO* 4.6 1.6 - - - +
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Residues in contact with GLN 65 (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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64A ARG* 1.3 78.4 - - - +
66A LEU* 1.3 60.6 + - - +
67A TYR 3.9 0.7 - - - -
73A HIS* 3.7 23.8 - - + +
88A ASP* 2.7 25.0 + - - +
89A HIS* 2.7 43.5 + - - +
90A SER* 4.3 2.6 + - - -
93A GLY 3.6 19.9 - - - +
94A ILE* 4.8 2.2 - - + -
95A LEU* 4.6 1.1 - - - -
188A LEU 3.3 0.3 - - - +
189A PRO* 3.4 4.5 - - - +
190A ARG* 2.7 43.2 + - + +
191A PRO 3.2 20.7 + - - +
192A VAL* 3.9 10.1 - - + -
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Residues in contact with LEU 66 (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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65A GLN* 1.3 71.2 - - - +
67A TYR* 1.3 63.1 + - - +
68A CYS 3.6 0.7 + - - -
72A PHE 3.6 0.9 - - - +
73A HIS* 3.1 5.6 - - - +
74A LEU* 3.0 43.3 + - + +
93A GLY 4.7 0.4 + - - -
95A LEU* 4.1 15.3 - - + +
97A PHE* 3.8 25.4 - - + -
107A ILE* 4.3 21.5 - - + -
116A LEU* 5.7 0.7 - - + -
148A TYR* 4.1 15.7 - - + +
164A VAL* 5.9 2.5 - - + -
187A PHE* 3.8 40.5 - - + -
188A LEU 3.8 9.9 - - - +
189A PRO* 3.8 11.7 - - + -
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Residues in contact with TYR 67 (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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65A GLN 3.9 0.2 - - - -
66A LEU* 1.3 72.9 - - - +
68A CYS* 1.3 74.1 + - - +
69A ARG* 4.6 1.1 + - - -
71A GLY* 3.5 34.7 + - - -
72A PHE 3.6 6.1 - - - -
73A HIS* 3.6 23.2 - + + +
145A TYR* 3.3 30.0 - + - -
187A PHE* 3.2 3.8 - - - -
188A LEU* 2.9 45.9 + - + +
190A ARG* 4.0 8.7 - - + -
143D ASN* 2.8 31.3 + - + -
144D TRP* 3.4 37.9 + + - -
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Residues in contact with CYS 68 (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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66A LEU 3.6 1.6 + - - -
67A TYR* 1.3 82.4 - - - +
69A ARG* 1.3 56.8 + - - +
70A THR* 2.9 23.3 - - - +
71A GLY* 2.6 29.5 + - - -
72A PHE 2.7 21.2 + - - +
166A LEU* 4.0 10.8 - - + -
184A PHE* 3.4 32.8 - - - -
186A HIS 3.3 11.0 - - - -
187A PHE* 3.5 23.1 - - + -
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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