Contacts of the strand formed by residues 61 - 68 (chain A) in PDB entry 1G86
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TYR* 5.3 1.6 - - - -
55A GLN* 4.2 9.7 + - - +
57A CYS* 2.8 63.2 + - + +
60A ARG* 1.3 90.7 - - + +
62A VAL* 1.3 65.6 + - - +
63A VAL* 3.8 25.2 - - - +
75A GLN* 5.0 5.7 + - - +
77A GLU* 4.0 21.2 + - - +
78A SER 3.5 13.2 - - - +
79A LYS* 4.2 13.9 - - + +
81A MET* 3.7 4.4 - - - +
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Residues in contact with VAL 62 (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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54A PHE* 3.6 31.4 - - + -
55A GLN 3.3 8.5 - - - +
56A VAL* 4.0 24.7 - - + -
61A ARG* 1.3 79.8 - - - +
63A VAL* 1.3 69.9 + - - +
64A MET* 4.4 6.7 - - + -
76A VAL 3.9 0.4 - - - +
77A GLU* 3.2 4.3 - - - +
78A SER* 2.9 32.5 + - - +
80A ASN 4.3 4.0 - - - +
81A MET* 4.3 2.2 - - + -
110A TYR* 3.3 43.7 - - + +
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Residues in contact with VAL 63 (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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53A HIS* 3.8 4.9 - - - +
54A PHE* 3.7 0.3 - - - -
55A GLN* 2.8 45.3 + - + +
57A CYS* 5.9 0.2 - - - -
61A ARG* 3.8 38.1 - - - +
62A VAL* 1.3 80.4 - - - +
64A MET* 1.3 69.3 + - - +
75A GLN* 3.4 32.5 - - + +
76A VAL 3.4 2.9 - - - -
77A GLU* 4.1 11.4 - - + -
153A NEQ 3.7 20.9 - - + +
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Residues in contact with MET 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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52A PHE* 3.9 19.5 - - + -
53A HIS* 3.1 10.1 - - - +
54A PHE* 3.8 25.6 - - + -
62A VAL* 4.4 10.5 - - + +
63A VAL* 1.3 79.5 - - - +
65A ASN* 1.3 64.1 + - - +
75A GLN* 3.6 1.4 - - - +
76A VAL* 2.7 60.7 + - + +
78A SER* 4.9 7.4 - - - -
102A VAL* 5.4 0.4 - - - -
110A TYR* 4.2 28.3 - - + -
111A THR 4.2 9.0 - - - +
112A PHE* 3.8 25.4 - - + -
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Residues in contact with ASN 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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52A PHE* 3.8 4.0 - - - -
53A HIS* 3.0 35.5 + - + -
64A MET* 1.3 74.9 - - - +
66A SER* 1.3 78.0 + - - +
72A TRP* 3.9 14.5 - - + +
73A LYS 2.9 33.6 + - - +
74A GLN 3.1 9.5 - - - +
75A GLN* 3.6 10.3 - - - +
112A PHE* 3.8 10.3 - - - -
115A ARG* 3.0 21.1 + - - +
153A NEQ 3.3 29.0 + - - +
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Residues in contact with SER 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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50A ILE* 3.3 15.5 - - - -
51A VAL* 3.7 13.5 - - - -
65A ASN* 1.3 80.5 + - - +
67A ARG* 1.3 60.0 + - - +
68A GLU* 2.7 29.9 + - - -
72A TRP* 3.4 9.9 - - - -
73A LYS* 2.9 27.9 + - - +
112A PHE* 4.8 0.2 - - - -
115A ARG* 3.1 25.0 + - - +
116A ILE* 5.5 0.9 - - - -
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Residues in contact with ARG 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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41A HIS* 3.9 0.2 - - - -
46A GLU 3.3 19.6 + - - -
47A GLU* 3.5 13.4 + - - +
48A SER 2.9 28.1 + - - -
49A ASP* 3.1 10.2 + - - +
50A ILE* 2.9 58.0 + - + +
66A SER* 1.3 73.7 - - - +
68A GLU* 1.3 60.2 + - - +
70A GLY* 3.7 34.4 - - - +
71A ALA 3.3 8.3 - - - +
72A TRP* 3.8 41.2 - - + +
116A ILE* 5.3 0.3 - - - +
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Residues in contact with GLU 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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49A ASP* 3.8 4.0 - - - -
66A SER* 2.7 28.2 + - - +
67A ARG* 1.3 76.3 - - - +
69A TYR* 1.3 79.3 + - + +
70A GLY 3.1 0.4 - - - -
71A ALA* 2.8 21.2 + - - +
73A LYS* 3.8 36.5 + - + +
115A ARG* 3.8 18.1 - - - +
116A ILE* 4.1 26.2 - - + +
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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