Contacts of the strand formed by residues 104 - 111 (chain A) in PDB entry 5DPQ
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A THR* 3.5 22.2 - - - +
77A LEU* 4.6 3.6 - - - +
78A ASP* 2.9 41.8 + - - -
80A ARG* 4.1 12.7 - - - +
82A VAL* 4.2 13.1 - - - +
96A VAL* 3.9 7.3 - - - +
97A GLN* 2.9 66.0 + - - +
99A GLY* 6.5 0.2 - - - -
101A LYS* 3.9 28.8 + - + +
102A GLU 4.4 1.6 - - - +
103A ASN* 1.3 76.2 - - - +
105A GLY* 1.3 59.0 + - - +
120A THR 3.3 9.6 - - - +
121A CYS* 4.6 8.3 - - + -
19B TYR* 4.6 7.7 + - - +
23B LEU* 3.5 24.2 - - - +
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Residues in contact with GLY 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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95A CYS 3.2 14.4 - - - -
96A VAL* 4.4 0.2 - - - -
97A GLN* 3.4 16.9 - - - +
103A ASN 4.2 0.6 - - - -
104A ARG* 1.3 77.6 - - - +
106A TRP* 1.3 64.0 + - - +
119A LEU* 3.7 1.4 - - - +
120A THR* 2.8 35.0 + - - +
19B TYR* 5.2 0.5 + - - -
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Residues in contact with TRP 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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64A PHE* 4.2 19.5 - + - -
70A PHE* 6.2 0.4 - + - -
86A VAL* 4.1 12.3 - - + -
93A LEU* 4.2 17.5 - - + -
94A VAL* 3.7 2.1 - - - +
95A CYS* 2.7 63.4 + - + +
97A GLN* 3.8 22.2 - - - -
105A GLY* 1.3 74.1 - - - +
107A LYS* 1.3 68.3 + - - +
108A GLN* 3.9 20.0 - - + -
117A LEU* 3.8 22.7 - - + -
118A GLU 3.1 14.6 - - - +
119A LEU* 4.0 18.4 - - + -
120A THR* 4.7 0.7 - - - +
201A ACT 4.1 27.8 + - + -
203A ACT 3.2 25.5 - - + +
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Residues in contact with LYS 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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92A VAL* 4.1 13.7 - - + -
93A LEU 3.0 12.3 - - - +
94A VAL* 4.4 11.4 - - + -
106A TRP* 1.3 78.5 - - - +
108A GLN* 1.3 61.5 + - - +
109A TRP* 3.7 24.0 - - + -
116A TYR 3.9 0.3 - - - +
117A LEU* 3.4 3.6 - - - +
118A GLU* 2.9 62.6 + - + +
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Residues in contact with GLN 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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64A PHE* 6.1 0.2 - - - -
92A VAL* 4.3 0.4 - - - +
93A LEU* 2.8 43.0 + - + +
106A TRP* 3.9 14.3 - - + -
107A LYS* 1.3 76.0 - - - +
109A TRP* 1.3 65.2 + - - +
115A LEU* 3.9 23.1 - - + +
116A TYR 3.2 11.9 - - - +
117A LEU* 3.7 13.5 - - + +
201A ACT 2.7 30.9 + - - +
4B GLN* 2.8 31.6 + - - +
40B LYS* 4.1 2.4 - - - +
42B ILE* 3.5 19.8 - - - +
49B PHE* 5.2 2.0 - - - -
51B THR* 5.7 0.6 - - - +
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Residues in contact with TRP 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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91A ASP* 4.4 5.6 - - - +
92A VAL* 3.8 30.7 - - + -
107A LYS* 3.7 41.5 - - + -
108A GLN* 1.3 80.8 - - - +
110A ILE* 1.3 68.0 + - - +
111A GLU* 3.6 32.5 + - + -
115A LEU* 3.4 2.9 - - - +
116A TYR* 2.7 69.8 + + + +
118A GLU* 3.8 29.6 - - + -
127A ARG* 4.0 17.5 - - - -
4B GLN* 3.8 6.3 - - - +
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Residues in contact with ILE 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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91A ASP* 5.1 9.0 + - - +
109A TRP* 1.3 79.2 - - - +
111A GLU* 1.3 73.2 + - - +
112A GLY 3.6 18.4 - - - +
114A LYS 3.3 8.1 - - - +
115A LEU* 3.7 28.5 - - + -
1B THR 4.9 15.0 + - - +
3B ASP 4.1 12.1 - - - +
4B GLN* 3.9 25.3 - - + +
8B TRP* 3.6 33.7 - - + -
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Residues in contact with GLU 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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109A TRP* 3.6 25.7 + - + +
110A ILE* 1.3 79.2 - - - +
112A GLY* 1.3 60.8 + - - +
113A ASP 3.3 0.3 + - - -
114A LYS* 2.9 34.8 + - - +
116A TYR* 3.8 19.3 + - + +
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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