Contacts of the strand formed by residues 106 - 115 (chain A) in PDB entry 6P59
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLN* 3.6 16.4 - - + +
11A LYS* 4.2 24.2 - - + +
12A PHE* 4.3 5.8 - - + -
17A PHE* 3.6 32.3 - - + -
102A ILE* 3.8 2.0 - - - -
103A LEU 2.8 32.5 + - - +
104A ASN 3.4 12.6 - - - +
105A GLY* 1.3 77.0 - - - +
107A CYS* 1.3 71.2 + - - +
108A VAL* 3.3 10.9 + - + +
127A PHE* 4.2 19.1 - - + -
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Residues in contact with CYS 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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8A GLN* 3.3 10.9 + - - +
101A MET 3.9 4.9 - - - -
102A ILE* 4.1 17.9 - - - -
105A GLY 4.7 0.4 - - - -
106A VAL* 1.3 71.1 - - - +
108A VAL* 1.3 63.8 + - - +
127A PHE* 3.9 10.2 - - - -
128A ASP* 3.2 33.9 + - + +
131A ARG* 4.0 17.7 - - + -
132A ALA* 3.6 30.5 - - + +
136A ASP* 4.0 15.3 - - - -
140A GLN* 4.6 5.8 - - - -
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Residues in contact with VAL 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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12A PHE* 4.0 12.1 - - + -
17A PHE* 3.8 27.6 - - + -
100A PRO* 3.5 1.0 - - - +
101A MET* 2.9 46.7 + - + +
103A LEU* 3.6 20.6 - - + -
106A VAL* 3.9 9.0 - - + +
107A CYS* 1.3 80.4 - - - +
109A ILE* 1.3 71.3 + - - +
125A LEU* 3.6 24.5 - - + -
126A GLU 3.3 12.6 - - - +
128A ASP* 3.9 5.2 - - - +
131A ARG* 5.2 1.2 + - - -
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Residues in contact with ILE 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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98A LYS* 4.1 27.1 - - + -
99A ALA 3.6 7.0 - - - +
100A PRO* 4.3 10.1 - - + -
108A VAL* 1.3 77.4 - - - +
110A TRP* 1.3 62.8 + - - +
111A LYS* 3.7 32.0 + - + +
125A LEU 3.8 0.2 - - - -
126A GLU* 2.8 47.4 + - + +
127A PHE 5.3 0.9 - - - +
128A ASP* 3.1 37.2 - - + +
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Residues in contact with TRP 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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21A LEU* 4.5 13.0 - - + +
23A ARG 4.8 0.6 + - - -
25A CYS* 4.1 25.5 - - - -
27A ILE* 3.4 35.4 - - + -
57A PHE* 6.1 1.1 - + + -
66A LEU* 3.5 30.0 - - + +
68A PHE* 5.5 0.7 - + - -
97A LEU* 4.4 16.8 - - + -
98A LYS* 3.3 1.9 - - - -
99A ALA* 2.7 48.7 + - + +
101A MET* 4.0 14.6 - - + -
108A VAL 4.2 0.4 - - - -
109A ILE* 1.3 73.0 - - - +
111A LYS* 1.3 62.4 + - - +
112A GLY* 3.6 15.9 - - - -
123A GLY* 3.7 26.2 - - - -
124A CYS* 3.8 11.5 - - - +
125A LEU* 3.5 31.1 - - + +
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Residues in contact with LYS 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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97A LEU 3.2 10.5 - - - +
98A LYS* 4.1 25.3 - - + +
109A ILE* 3.7 28.2 + - + +
110A TRP* 1.3 83.1 - - - +
112A GLY* 1.3 58.4 + - - +
123A GLY* 3.3 0.9 - - - -
124A CYS* 3.1 35.7 + - - +
126A GLU* 3.7 29.3 + - - +
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Residues in contact with GLY 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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96A TYR* 3.4 7.7 - - - +
97A LEU* 2.7 37.2 + - - +
110A TRP* 3.6 10.8 - - - -
111A LYS* 1.3 76.4 - - - +
113A TRP* 1.3 65.8 + - - +
122A MET 3.3 13.7 - - - -
123A GLY* 3.7 4.3 - - - -
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Residues in contact with TRP 113 (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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27A ILE* 4.0 1.5 - - - +
94A LYS* 3.8 29.3 - - + +
95A VAL 3.1 13.9 - - - +
96A TYR* 3.9 32.3 - + + -
97A LEU* 4.6 3.0 - - - +
112A GLY* 1.3 79.9 - - - +
114A ILE* 1.3 72.9 + - - +
115A ASP 3.7 12.8 - - - -
118A ARG* 3.1 34.5 - - - -
121A GLY* 3.3 24.4 - - - -
122A MET* 3.1 47.1 + - + +
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Residues in contact with ILE 114 (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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27A ILE* 3.5 30.7 - - + +
28A LYS 4.8 0.2 - - - +
29A TYR* 5.2 0.7 - - + -
44A PHE* 4.3 16.4 - - + -
57A PHE* 3.3 36.3 - - + -
94A LYS* 3.3 3.5 - - - +
95A VAL* 2.9 42.9 + - + +
97A LEU* 4.0 7.0 - - + -
113A TRP* 1.3 84.8 - - - +
115A ASP* 1.3 74.8 + - - +
119A LEU* 3.9 20.0 - - + +
120A ASP* 3.8 4.0 - - - -
121A GLY 3.8 10.5 - - - +
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Residues in contact with ASP 115 (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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93A GLY* 2.9 21.7 - - - +
94A LYS* 4.3 10.2 - - + +
113A TRP* 3.7 3.3 - - + -
114A ILE* 1.3 72.4 - - - +
116A LEU* 1.3 60.1 + - - +
117A GLN* 3.3 21.4 + - - +
118A ARG* 2.6 57.1 + - + +
119A LEU* 2.7 34.7 + - - -
120A ASP 3.1 11.7 + - - +
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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