Contacts of the strand formed by residues 102 - 110 (chain A) in PDB entry 6B0B
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.4 6.7 - - + -
63A ILE* 6.0 4.5 - - + -
68A LEU* 4.8 9.6 - - + -
74A TYR* 3.6 34.3 - - + +
76A VAL* 4.1 17.0 - - + -
95A PHE* 5.6 6.5 - - + -
96A ILE* 3.8 26.6 - - + +
99A HIS* 3.7 26.8 - - + +
100A ASP* 3.1 3.5 - - - +
101A HIS* 1.3 115.0 - - + +
103A ASN* 1.3 70.6 + - - +
104A LEU 4.3 0.4 - - - -
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Residues in contact with ASN 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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73A CYS* 5.0 15.2 - - - +
74A TYR 2.9 13.0 + - - +
75A GLN* 2.9 36.1 - - - +
76A VAL* 2.9 17.6 + - - +
96A ILE* 5.6 0.2 - - - -
100A ASP* 4.6 7.3 + - - +
102A LEU* 1.3 82.7 - - - +
104A LEU* 1.3 60.0 + - - +
130A GLN 5.9 1.3 - - - +
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Residues in contact with LEU 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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59A PHE* 5.1 11.9 - - + -
75A GLN* 4.1 1.3 - - - -
76A VAL* 3.2 39.7 - - + +
78A CYS* 3.9 13.7 - - + -
92A LEU* 3.8 26.0 - - + -
96A ILE* 4.5 18.0 - - + +
102A LEU 4.3 0.4 - - - -
103A ASN* 1.3 74.1 - - - +
105A ARG* 1.3 71.9 + - - +
106A ILE* 3.8 23.6 - - + -
130A GLN 4.5 2.3 + - - +
131A VAL* 3.2 35.2 - - + +
132A PRO* 3.5 13.7 - - - +
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Residues in contact with ARG 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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75A GLN* 3.2 34.3 - - - +
76A VAL 2.9 9.4 + - - +
77A THR* 3.5 23.2 + - - +
78A CYS 2.9 27.5 + - - +
79A TYR* 3.2 25.3 + - - -
104A LEU* 1.3 78.7 - - - +
106A ILE* 1.3 60.9 + - - +
107A PHE* 3.5 32.2 - - + -
131A VAL* 4.2 1.1 - - - -
132A PRO* 4.2 13.5 - - + +
140A GLU* 5.6 0.8 + - - -
143A ASP* 5.3 1.0 + - - -
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Residues in contact with ILE 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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30A LEU* 6.1 0.7 - - + -
59A PHE* 6.4 0.2 - - + -
78A CYS* 3.6 33.0 - - + +
80A LEU* 3.7 22.9 - - + -
84A PRO* 4.8 14.1 - - + -
92A LEU* 4.5 13.7 - - + -
104A LEU* 3.8 19.5 - - + -
105A ARG* 1.3 72.5 - - - +
107A PHE* 1.3 64.7 + - - +
108A ALA* 4.7 1.6 - - + +
126A LEU* 4.9 2.7 - - + -
131A VAL* 3.6 17.2 - - + +
132A PRO 3.6 7.3 + - - +
133A VAL* 3.5 30.3 - - + -
134A GLU 3.2 24.1 + - - +
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Residues in contact with PHE 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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13A PHE* 5.8 0.2 - - - -
78A CYS 2.9 8.9 + - - -
79A TYR* 3.2 37.0 - + + +
80A LEU* 2.9 27.1 + - - +
105A ARG* 3.5 50.3 - - + -
106A ILE* 1.3 77.2 - - - +
108A ALA* 1.3 62.0 + - - +
132A PRO* 5.1 5.6 - - + -
134A GLU* 3.2 34.5 - - + +
135A VAL 4.1 8.1 - - - -
136A MET* 4.8 4.1 - - + +
140A GLU* 3.2 30.5 - - + -
174A LYS* 5.8 1.8 - - - -
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Residues in contact with ALA 108 (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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80A LEU* 3.1 20.4 - - + +
83A SER* 4.0 26.7 - - - +
84A PRO* 5.2 1.1 - - + -
106A ILE* 4.1 3.5 - - + +
107A PHE* 1.3 73.9 - - - +
109A SER* 1.3 59.3 + - - +
110A ARG 4.1 7.4 - - - +
111A LEU* 5.1 1.8 - - + -
133A VAL* 6.0 3.1 - - + -
134A GLU 3.4 7.2 + - - +
135A VAL* 3.1 12.1 - - + +
136A MET* 2.4 36.9 + - - +
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Residues in contact with SER 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 PHE* 2.5 52.2 + - - -
15A ASN* 3.2 6.3 + - - -
80A LEU 2.9 7.0 + - - -
81A THR* 3.1 13.8 + - - -
108A ALA* 1.3 74.0 - - - +
110A ARG* 1.3 57.2 + - - +
135A VAL* 3.7 5.6 - - - +
136A MET* 3.5 20.8 - - - +
141A PHE* 3.1 14.7 - - - -
169A ASN* 4.8 0.5 - - - +
173A ILE* 3.6 15.8 - - - +
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Residues in contact with ARG 110 (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 ASN* 3.2 33.4 - - + +
16A LYS 5.5 4.2 + - - -
17A ARG* 6.3 1.4 - - - +
81A THR 2.9 7.5 + - - +
82A TRP* 3.4 31.4 - - + -
83A SER* 2.9 21.1 + - - -
108A ALA* 4.1 1.8 - - - +
109A SER* 1.3 73.4 - - - +
111A LEU* 1.3 93.6 + - - +
112A TYR 2.9 8.3 + - - -
113A TYR* 4.9 0.4 - - - -
115A TRP* 3.6 31.7 - - - -
173A ILE* 3.5 34.4 - - - +
176A ARG* 4.9 7.1 - - - +
0C U 3.1 23.8 + - - +
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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