Contacts of the strand formed by residues 104 - 112 (chain A) in PDB entry 3GJ9
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 VAL 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.6 31.2 - - + +
18A ILE 3.4 5.4 - - - +
19A HIS* 3.4 35.2 - - + +
20A LYS* 4.9 0.4 - - - -
81A ASN* 3.2 16.8 + - - +
102A GLU* 3.1 11.3 - - - +
103A GLU* 1.3 94.3 - - + +
105A VAL* 1.3 70.6 + - - +
106A ARG* 4.2 20.9 + - + +
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Residues in contact with VAL 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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16A VAL 3.7 0.3 - - - +
17A GLU* 3.5 2.1 - - - -
18A ILE* 3.0 48.7 + - + +
20A LYS* 3.8 21.3 - - - +
29A LEU* 3.6 24.2 - - + -
80A VAL* 4.2 15.3 - - + -
81A ASN* 3.5 7.4 - - - +
96A ARG 4.7 1.6 - - - +
97A LEU* 4.1 15.7 - - + +
102A GLU* 4.9 1.1 - - - +
104A VAL* 1.3 81.2 - - - +
106A ARG* 1.3 61.5 + - - +
107A LEU* 3.6 20.1 + - + +
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Residues in contact with ARG 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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15A ARG* 5.2 11.2 - - + +
16A VAL 3.7 3.8 - - - -
17A GLU* 3.5 44.8 + - + +
80A VAL* 3.6 2.3 - - - -
81A ASN* 2.6 42.8 + - - +
104A VAL* 4.2 14.8 + - + +
105A VAL* 1.3 71.2 - - - +
107A LEU* 1.3 62.5 + - - +
126A CL 3.3 20.4 - - + +
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Residues in contact with LEU 107 (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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15A ARG* 3.0 10.4 - - - +
16A VAL* 2.6 44.4 + - + +
18A ILE* 3.7 29.4 - - + -
31A PHE* 4.5 13.7 - - + -
71A LEU* 4.4 17.9 - - + -
77A ILE* 4.4 12.3 - - + -
79A GLN 3.5 2.2 - - - -
80A VAL* 3.7 27.6 - - + -
97A LEU* 4.1 4.9 - - + -
105A VAL* 3.8 22.4 - - + -
106A ARG* 1.3 78.4 - - - +
108A LEU* 1.3 61.3 - - - +
109A VAL* 4.0 10.8 - - + -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.3 35.4 - - + -
14A GLN 3.8 4.3 - - - +
15A ARG* 4.8 24.9 - - + +
77A ILE* 3.6 0.7 - - - -
78A MET* 2.7 43.5 + - + -
79A GLN* 2.9 52.6 + - + +
106A ARG 5.5 0.2 - - - +
107A LEU* 1.3 74.1 - - - +
109A VAL* 1.3 55.6 + - - +
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Residues in contact with VAL 109 (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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13A VAL* 3.3 6.1 - - - +
14A GLN* 2.7 56.1 + - + +
16A VAL* 4.3 13.0 - - + -
71A LEU* 4.5 12.8 - - + -
75A ASP* 4.2 23.1 - - + +
76A LYS 3.1 17.0 - - - +
77A ILE* 4.0 15.3 - - + -
78A MET* 4.1 1.6 - - - -
107A LEU* 4.1 18.6 - - + -
108A LEU* 1.3 79.9 - - - +
110A THR* 1.3 65.5 + - - +
111A ARG* 4.3 7.4 - - - +
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Residues in contact with THR 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ALA* 4.9 11.4 - - + -
12A VAL 3.0 14.6 - - - +
13A VAL* 4.1 14.1 - - + -
74A GLY 4.6 0.7 - - - +
75A ASP* 3.7 1.4 - - - -
76A LYS* 3.0 44.1 + - - +
78A MET* 3.7 27.1 - - + +
109A VAL* 1.3 80.9 - - - +
111A ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 111 (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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11A ALA* 4.4 4.0 - - - -
12A VAL* 3.0 35.5 + - + +
14A GLN* 3.4 27.2 + - + +
16A VAL* 4.4 6.3 - - - +
70A GLY 3.0 24.2 + - - -
71A LEU* 4.2 0.8 - - - +
72A GLN* 2.9 33.4 - - - +
74A GLY 5.2 3.1 - - - +
75A ASP* 2.6 51.1 + - - +
109A VAL* 4.3 14.0 - - + +
110A THR* 1.3 73.9 - - - +
112A GLN* 1.3 59.0 + - - +
113A SER* 2.6 20.0 + - - -
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Residues in contact with GLN 112 (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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10A THR 4.6 2.0 - - - -
11A ALA* 4.6 8.9 - - - +
46A PHE 6.1 0.4 - - - +
74A GLY 5.8 0.4 + - - -
111A ARG* 1.3 73.6 - - - +
113A SER* 1.3 54.3 + - - +
114A LEU* 2.8 23.0 + - - +
79B GLN* 5.9 2.9 - - - +
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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