Contacts of the helix formed by residues 90 - 100 (chain A) in PDB entry 2JIF
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.2 20.5 - - + +
82A THR* 4.7 13.7 - - + +
83A MET* 3.4 30.4 - - + +
86A ASN* 5.0 3.6 + - - -
88A LYS* 4.5 26.0 + - - +
89A MET* 1.3 73.2 - - - +
91A LYS* 1.3 66.5 + - - +
92A SER* 3.8 17.7 + - - +
93A VAL* 3.1 17.3 + - + +
94A ILE* 3.3 14.2 + - - +
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Residues in contact with LYS 91 (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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88A LYS* 5.9 1.8 - - - +
89A MET 3.7 3.2 + - - -
90A GLU* 1.3 73.9 + - - +
92A SER* 1.3 57.6 + - - +
94A ILE* 3.1 12.8 + - + +
95A GLN* 2.8 56.8 + - + +
213A HIS* 5.8 4.7 - - + +
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 5.5 0.3 - - - -
75A GLN* 5.2 6.0 + - - +
79A LEU* 3.7 23.2 - - - +
90A GLU* 3.8 7.6 + - - +
91A LYS* 1.3 78.9 - - - +
93A VAL* 1.3 59.7 + - - +
95A GLN* 3.7 14.2 + - - +
96A GLY* 2.9 24.8 + - - -
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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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71A PHE* 4.1 5.1 - - + -
75A GLN* 4.0 12.3 - - - +
76A ILE* 4.1 14.6 - - + -
79A LEU* 3.8 28.3 - - + -
83A MET* 4.2 12.3 - - + -
89A MET* 4.2 9.6 - - - -
90A GLU* 3.1 15.3 + - + +
92A SER* 1.3 78.9 + - - +
94A ILE* 1.3 61.1 + - - +
96A GLY* 3.2 1.9 + - - -
97A LEU* 2.9 30.6 + - + +
135A VAL* 3.9 39.3 - - + -
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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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89A MET* 3.7 26.5 - - + -
90A GLU 3.7 11.4 - - - +
91A LYS* 3.1 12.9 + - + +
93A VAL* 1.3 74.4 - - - +
95A GLN* 1.3 67.8 + - + +
97A LEU* 3.2 18.5 + - + +
98A PHE* 3.2 42.2 + - + -
138A PHE* 3.8 27.1 - - + -
171A VAL* 4.4 4.3 - - + -
213A HIS* 3.9 37.2 - - + +
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Residues in contact with GLN 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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91A LYS* 2.8 43.8 + - + +
92A SER* 3.8 13.6 + - - +
94A ILE* 1.3 74.2 - - + +
96A GLY* 1.3 57.4 + - - +
98A PHE* 3.3 10.5 + - - +
99A GLN* 2.9 30.1 + - - +
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Residues in contact with GLY 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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71A PHE* 3.7 19.3 - - - -
92A SER 2.9 16.9 + - - -
93A VAL 3.5 3.8 - - - -
94A ILE 3.1 0.2 - - - -
95A GLN* 1.3 74.4 - - - +
97A LEU* 1.3 58.1 + - - +
99A GLN* 3.8 9.8 - - - +
100A GLN* 2.9 35.7 + - - +
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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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71A PHE* 3.8 14.7 - - + -
89A MET* 6.0 0.7 - - - -
93A VAL* 2.9 20.4 + - + +
94A ILE* 3.2 9.4 + - + +
96A GLY* 1.3 74.5 - - - +
98A PHE* 1.3 61.0 + - - +
100A GLN 3.6 0.3 + - - -
101A GLY 3.4 1.7 + - - -
102A LEU* 2.8 58.0 + - + +
103A MET* 3.8 17.2 + - + -
128A LEU* 4.0 20.4 - - + -
135A VAL* 3.9 23.6 - - + +
138A PHE* 3.7 32.1 - - + -
139A CYS* 4.7 4.5 - - + -
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Residues in contact with PHE 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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94A ILE* 3.2 43.5 + - + -
95A GLN* 3.6 9.2 - - - +
97A LEU* 1.3 78.4 - - - +
99A GLN* 1.3 63.4 + - - +
101A GLY* 3.1 14.7 + - - -
103A MET* 3.6 37.2 - - + -
142A GLN* 3.9 0.2 - - - -
166A LEU 3.4 23.3 - - - -
167A THR 3.8 13.3 - - - +
168A THR* 3.3 31.3 - - - +
169A GLU* 3.6 32.8 - - - -
170A LYS 3.7 11.4 - - - -
171A VAL* 3.9 7.0 - - + -
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Residues in contact with GLN 99 (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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71A PHE* 5.5 1.0 - - - -
95A GLN 2.9 18.1 + - - +
96A GLY* 3.8 9.2 - - - +
98A PHE* 1.3 77.3 - - - +
100A GLN* 1.3 85.1 + - - +
101A GLY* 3.2 1.3 + - - -
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Residues in contact with GLN 100 (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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67A SER* 4.3 17.4 + - - -
68A VAL* 5.9 0.2 - - - +
71A PHE* 3.8 37.6 - - + +
96A GLY 2.9 19.7 + - - +
99A GLN* 1.3 100.7 + - - +
101A GLY* 1.3 61.0 + - - +
102A LEU* 3.3 26.5 + - + +
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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