Contacts of the strand formed by residues 116 - 123 (chain A) in PDB entry 6DC0
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 GLU 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ARG* 2.6 42.0 + - + -
108A ALA 3.8 4.7 - - - +
109A LEU* 3.3 26.3 - - + +
114A GLY 3.5 3.4 + - - +
115A ARG* 1.3 73.9 - - - +
117A LEU* 1.3 61.4 + - - +
118A ARG* 3.2 18.6 + - - +
162A LYS* 3.2 50.0 + - + +
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Residues in contact with LEU 117 (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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94A TYR* 3.8 29.4 - - + +
108A ALA* 2.8 36.4 + - + +
115A ARG* 3.7 53.4 - - + +
116A GLU* 1.3 72.5 - - - +
118A ARG* 1.3 85.9 + - - +
147A VAL* 3.8 25.1 - - + -
159A PHE* 4.5 6.7 - - + -
160A PHE 3.5 16.6 - - - +
161A GLU* 3.9 5.6 - - - +
162A LYS* 4.8 1.3 - - - +
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Residues in contact with ARG 118 (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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99A LEU* 3.4 32.3 - - - +
105A VAL* 4.2 13.5 - - + -
106A SER 3.8 2.2 - - - -
107A ARG* 3.8 20.7 - - - +
116A GLU* 3.2 31.3 + - - +
117A LEU* 1.3 111.6 + - - +
119A CYS* 1.3 59.3 + - - +
120A LYS* 4.3 1.1 - - + -
159A PHE* 3.5 3.5 - - - -
160A PHE* 2.7 52.7 + - + +
161A GLU 4.5 3.0 - - - +
162A LYS* 3.2 43.7 - - + +
163A ASP* 5.1 7.3 + - - +
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Residues in contact with CYS 119 (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 LEU* 3.8 21.8 - - + -
104A HIS 3.7 1.6 - - - +
105A VAL* 3.4 3.7 - - - +
106A SER* 2.9 38.6 + - - +
108A ALA* 4.1 8.5 - - + -
118A ARG* 1.3 75.6 - - - +
120A LYS* 1.3 65.5 + - - +
121A VAL* 3.9 1.3 + - - +
157A TYR* 3.9 20.6 - - - -
158A VAL 3.4 6.5 - - - -
159A PHE* 3.3 39.7 - - + -
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Residues in contact with LYS 120 (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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102A ARG* 5.9 1.8 - - - +
104A HIS* 3.8 6.3 - - + +
105A VAL* 4.1 24.3 - - + +
118A ARG* 4.3 0.6 - - + -
119A CYS* 1.3 73.2 - - - +
121A VAL* 1.3 62.2 + - - +
122A PHE* 3.9 21.9 + - + -
156A ALA 4.0 0.3 - - - +
157A TYR* 3.7 2.3 - - - -
158A VAL* 2.9 35.1 + - - +
160A PHE* 3.8 30.1 - - + -
224A GLU* 5.3 3.3 + - - +
225A SER* 3.3 21.4 + - - -
227A GLU* 3.3 38.8 + - + +
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Residues in contact with VAL 121 (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 LEU* 4.7 7.6 - - + -
104A HIS* 3.2 41.6 + - + +
106A SER* 5.3 2.9 - - - +
119A CYS* 4.5 7.2 - - - +
120A LYS* 1.3 74.9 - - - +
122A PHE* 1.3 69.4 + - - +
123A PRO* 4.9 0.7 - - - +
155A LYS* 3.6 28.9 - - + +
156A ALA 3.3 15.7 - - - +
157A TYR* 3.5 33.4 - - + +
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Residues in contact with PHE 122 (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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120A LYS* 3.9 27.1 - - + -
121A VAL* 1.3 81.1 - - - +
123A PRO* 1.3 73.9 - - + +
126A HIS 4.9 0.9 - - - -
127A TYR* 4.0 23.8 - - + +
130A LYS* 3.7 35.0 - - + -
131A ILE* 4.8 3.4 - - + -
155A LYS* 3.1 11.6 - - - +
156A ALA 2.7 36.6 + - - +
158A VAL* 3.7 32.3 - - + -
160A PHE* 5.8 0.4 - + - -
227A GLU* 3.5 23.1 - - + -
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Residues in contact with PRO 123 (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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121A VAL 4.9 0.4 - - - +
122A PHE* 1.3 89.2 - - + +
124A ILE* 1.3 66.4 + - + +
125A LYS* 3.1 6.7 - - + +
126A HIS* 2.9 34.5 + - + +
127A TYR 3.2 8.0 + - - -
154A THR* 3.5 14.4 - - + +
155A LYS* 4.2 4.5 - - + +
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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