Contacts of the strand formed by residues 92 - 98 (chain A) in PDB entry 1NFK
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ALA* 1.3 82.0 - - - +
93A VAL* 1.3 63.9 + - - +
94A ILE* 6.0 0.2 - - + -
122A THR* 5.0 14.8 - - + -
123A VAL 3.4 7.4 - - - +
124A THR* 3.3 27.4 - - + +
125A ALA 4.3 0.4 - - - +
179A GLU* 5.2 8.5 - - - +
215A THR 3.9 0.5 - - - +
216A ALA* 3.3 3.5 - - - +
217A PHE* 2.8 41.8 + - + +
225A PHE* 3.7 37.9 - - + -
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Residues in contact with VAL 93 (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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42A LEU* 4.8 4.7 - - + -
82A VAL* 4.6 8.5 - - + -
84A ILE* 4.4 18.8 - - + -
92A LYS* 1.3 79.7 - - - +
94A ILE* 1.3 70.7 + - - +
95A VAL* 5.1 1.3 - - - +
121A CYS 4.0 0.3 - - - +
122A THR* 3.5 1.6 - - - -
123A VAL* 2.6 50.0 + - + +
125A ALA* 4.7 4.0 - - + -
132A VAL* 3.8 26.9 - - + -
134A PHE* 4.4 15.9 - - + -
214A PHE* 4.5 9.9 - - + -
215A THR 3.4 15.9 - - - +
216A ALA* 4.6 3.4 - - + -
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Residues in contact with ILE 94 (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 LYS* 5.6 0.7 - - + -
93A VAL* 1.3 76.3 - - - +
95A VAL* 1.3 61.4 + - - +
96A GLN* 3.7 25.8 - - + +
120A VAL* 4.4 4.9 - - + -
121A CYS 3.2 7.6 - - - +
122A THR* 3.8 28.7 - - + +
163A TYR* 3.9 36.1 - - + -
164A ASN* 4.9 2.5 - - - +
179A GLU* 4.9 3.4 - - - +
213A MET 3.6 0.7 - - - +
214A PHE* 3.3 4.5 - - - -
215A THR* 2.8 59.9 + - + +
217A PHE* 4.2 19.7 - - + -
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Residues in contact with VAL 95 (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 VAL 5.1 0.2 - - - +
94A ILE* 1.3 76.4 - - - +
96A GLN* 1.3 74.4 + - - +
111A LEU* 4.1 17.4 - - + +
119A GLY 4.3 0.5 - - - +
120A VAL* 3.6 3.3 - - - +
121A CYS* 3.1 41.7 + - + +
134A PHE* 3.2 44.6 - - + -
137A LEU* 4.9 5.8 - - + -
212A LEU* 4.4 15.3 - - + -
213A MET 3.2 9.6 - - - +
214A PHE* 4.0 20.2 - - + -
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Residues in contact with GLN 96 (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 ILE* 3.7 24.0 - - + +
95A VAL* 1.3 82.2 - - - +
97A LEU* 1.3 60.8 + - - +
98A VAL* 3.8 4.9 + - + -
106A LEU* 3.8 25.3 - - + +
111A LEU* 4.0 9.2 - - - +
119A GLY 4.3 4.9 - - - +
120A VAL* 4.1 19.0 - - + +
158A ALA* 5.3 1.0 - - - +
163A TYR* 3.8 21.5 + - - +
164A ASN* 3.7 18.9 - - - +
168A LEU* 3.8 12.0 - - - +
212A LEU* 3.6 4.5 - - - -
213A MET* 2.9 45.5 + - + +
215A THR* 4.4 0.5 + - - -
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Residues in contact with LEU 97 (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 GLN* 1.3 72.6 - - - +
98A VAL* 1.3 63.5 + - - +
106A LEU* 4.0 5.2 - - - +
107A HIS* 2.9 33.7 + - + +
109A HIS* 3.5 33.7 - - + +
110A SER 3.8 2.2 - - - -
111A LEU* 3.6 32.9 - - + +
119A GLY 4.5 4.5 + - - +
139A ILE* 3.8 19.5 - - + -
210A VAL* 3.7 21.1 - - + -
211A ARG 3.2 15.7 - - - +
212A LEU* 3.6 22.2 - - + -
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Residues in contact with VAL 98 (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 GLN* 3.8 4.0 + - + +
97A LEU* 1.3 78.3 - - - +
99A THR* 1.3 62.5 + - - +
104A ILE* 4.4 10.8 - - + -
105A HIS 3.1 19.5 - - - +
106A LEU* 4.7 0.7 - - - -
107A HIS* 3.8 7.4 + - - +
168A LEU* 3.7 30.1 - - + -
210A VAL* 3.8 1.7 - - - +
211A ARG* 2.9 35.1 + - + +
213A MET* 3.8 24.0 - - + -
233A VAL* 3.7 29.6 - - + -
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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