Contacts of the strand formed by residues 100 - 106 (chain A) in PDB entry 3G85
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 ASN 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.6 39.1 + - - +
66A PRO 3.0 6.9 + - - +
67A THR* 3.3 26.1 + - + +
68A ILE 2.8 24.3 + - - -
99A TYR* 1.3 77.0 + - - +
101A VAL* 1.3 65.3 - - - +
102A VAL* 5.4 2.0 - - + -
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Residues in contact with VAL 101 (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 ILE* 3.2 23.1 - - + +
70A LEU* 5.0 2.9 - - + -
85A LEU* 6.2 2.2 - - + -
88A LEU* 3.8 31.4 - - + -
92A LEU* 3.5 29.2 - - + +
99A TYR 4.0 1.0 + - - -
100A ASN* 1.3 78.7 - - - +
102A VAL* 1.3 81.4 + - - +
103A ILE* 4.8 6.3 - - + -
127A ILE* 6.5 0.4 - - + -
307A ILE* 4.5 13.2 - - + -
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Residues in contact with VAL 102 (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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67A THR* 3.8 22.9 - - + -
68A ILE 3.0 5.9 + - - +
69A ALA* 3.4 2.3 - - + -
70A LEU* 2.8 25.3 + - - -
100A ASN* 5.4 2.5 - - + -
101A VAL* 1.3 83.3 - - - +
103A ILE* 1.3 66.2 + - - +
104A CYS* 3.6 25.6 - - - -
123A PHE* 3.9 15.9 - - + -
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Residues in contact with ILE 103 (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 LEU* 3.5 26.7 - - + +
72A TRP* 4.2 18.4 - - + -
81A ILE* 3.5 35.0 - - + -
85A LEU* 4.2 25.6 - - + -
88A LEU* 5.3 1.1 - - + -
101A VAL* 4.8 7.6 - - + -
102A VAL* 1.3 78.8 - - - +
104A CYS* 1.3 63.2 + - - +
105A PRO* 3.3 17.3 - - + +
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Residues in contact with CYS 104 (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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69A ALA* 4.1 8.7 - - - -
70A LEU 2.8 9.5 + - - +
71A TYR* 3.4 26.4 - - + -
72A TRP* 2.9 22.8 + - - -
102A VAL* 3.6 25.6 - - - -
103A ILE* 1.3 70.9 - - - +
105A PRO* 1.3 68.5 - - - +
106A TYR* 3.4 4.3 + - - -
114A GLU* 4.9 4.7 - - - +
123A PHE* 3.9 23.8 - - - -
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Residues in contact with PRO 105 (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 TRP* 3.3 19.7 - - + +
103A ILE* 3.3 19.5 - - + +
104A CYS* 1.3 86.0 - - - +
106A TYR* 1.3 60.6 + - - +
114A GLU* 4.5 4.5 - - - +
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Residues in contact with TYR 106 (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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71A TYR* 3.6 21.8 - + + -
72A TRP 3.0 25.1 + - - +
73A SER* 3.4 38.6 - - - -
74A SER* 2.9 27.2 + - - -
104A CYS 3.6 4.7 - - - +
105A PRO* 1.3 75.4 - - - +
107A LYS* 1.3 82.2 + - - +
109A ASP 4.7 1.3 - - - -
110A CYS* 3.9 2.0 - - + +
111A LEU* 3.6 39.1 - - + +
114A GLU* 3.4 25.1 - - + +
128A ILE* 3.6 20.4 - - - +
130A ASN 3.9 5.9 + - - -
131A ILE* 4.3 3.5 - - - -
132A SER 5.0 0.3 + - - -
135A ASP* 3.8 7.4 + - - -
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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