Contacts of the strand formed by residues 114 - 120 (chain A) in PDB entry 7NPA
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 LYS 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ASP* 4.1 0.7 - - - -
111A GLU* 2.9 39.8 + - + +
112A CYS* 3.2 4.8 + - - +
113A TRP* 1.3 76.9 - - - +
115A PRO* 1.3 71.9 - - + +
116A VAL* 3.6 1.4 + - - +
207A TYR* 3.1 47.3 + - + +
211A LYS* 5.9 0.8 - - - +
222A ASP* 5.7 0.2 + - - -
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Residues in contact with PRO 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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108A VAL* 3.7 19.3 - - + -
109A GLY 3.3 8.3 - - - +
110A ASP* 4.2 1.8 - - + -
113A TRP 3.2 9.9 - - - +
114A LYS* 1.3 87.1 - - + +
116A VAL* 1.3 60.1 + - - +
133A LYS* 4.0 15.3 - - + -
135A THR* 3.2 28.0 - - - +
136A VAL 3.5 20.9 - - - +
137A SER* 4.4 7.6 - - - -
207A TYR* 5.0 3.6 - - + -
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Residues in contact with VAL 116 (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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108A VAL* 3.4 5.9 - - - -
109A GLY* 2.9 48.8 + - - -
110A ASP* 3.6 11.4 - - - +
111A GLU* 4.8 12.1 - - + +
114A LYS 4.6 1.3 - - - +
115A PRO* 1.3 75.8 - - - +
117A SER* 1.3 75.2 + - - +
118A LEU* 3.6 20.0 + - + +
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Residues in contact with SER 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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106A ILE* 4.2 6.1 - - - +
107A VAL 3.6 5.8 + - - -
108A VAL* 4.8 2.5 - - - +
116A VAL* 1.3 81.8 - - - +
118A LEU* 1.3 60.5 + - - +
138A THR* 3.5 38.3 + - - +
139A LEU* 3.4 4.9 - - - -
140A GLU* 3.3 11.5 + - - +
141A ALA* 2.8 35.1 + - - +
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Residues in contact with LEU 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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105A ALA 3.3 1.0 - - - +
106A ILE* 3.3 6.6 - - - -
107A VAL* 2.7 37.8 + - + +
109A GLY* 3.8 27.6 - - - +
116A VAL* 3.8 23.3 - - + +
117A SER* 1.3 81.4 + - - +
119A ILE* 1.3 58.7 + - - +
120A VAL* 3.9 14.8 - - + -
125A ASP 5.5 1.1 - - - +
128A ASN* 5.7 3.4 - - + +
129A THR* 3.9 14.8 - - + -
141A ALA* 3.3 7.5 - - - +
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Residues in contact with ILE 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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104A GLY* 4.0 5.2 - - - -
105A ALA 3.4 23.6 - - - +
106A ILE* 3.7 23.1 - - + -
118A LEU* 1.3 73.1 - - - +
120A VAL* 1.3 61.8 + - - +
121A GLN* 4.2 6.6 + - + +
125A ASP* 5.6 0.5 - - - +
141A ALA* 3.5 5.5 - - + +
144A THR* 4.1 20.9 - - + -
145A ALA* 4.1 7.0 - - + +
148A MET* 4.1 26.2 - - + +
150A LEU* 3.7 32.5 - - + -
153A VAL* 4.3 2.7 - - + -
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Residues in contact with VAL 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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97A LEU* 4.5 4.5 - - + +
104A GLY* 3.1 4.3 - - - -
105A ALA* 2.8 47.3 + - + +
107A VAL* 3.7 18.8 - - + -
118A LEU* 4.2 13.2 - - + -
119A ILE* 1.3 77.5 - - - +
121A GLN* 1.3 60.6 + - - +
122A ASN 4.5 2.0 - - - +
125A ASP* 3.8 37.2 - - + +
126A LEU* 3.6 33.0 - - + +
129A THR* 4.4 2.0 - - + -
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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