Contacts of the helix formed by residues 99 - 107 (chain A) in PDB entry 1JQI
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 TYR 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A VAL 3.0 10.8 + - - +
95A ASN* 3.6 17.9 - - - +
98A LEU* 1.3 75.2 - - - +
100A LEU* 1.3 92.2 + - + +
102A PRO* 3.2 16.3 - - - +
103A ILE* 3.4 29.6 - - + +
115A TRP* 2.8 39.9 + - - +
119A PHE* 3.5 29.6 - + - -
126A GLY* 3.7 25.1 - - - -
127A CYS 4.0 9.8 + - - +
170A ALA* 3.5 30.9 - - + +
171A THR* 4.4 1.8 - - - -
172A VAL* 4.0 16.4 - - + +
190A LEU* 4.9 2.5 - - + -
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Residues in contact with LEU 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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56A LEU 3.4 26.0 - - - +
57A ALA* 3.8 20.4 - - + -
60A VAL* 3.8 17.0 - - + -
95A ASN* 3.1 21.3 + - - +
96A ASN* 3.7 6.3 - - - +
99A TYR* 1.3 103.4 - - + +
101A GLY* 1.3 66.1 + - - +
103A ILE 3.3 0.5 + - - -
104A LEU* 2.9 29.1 + - - +
116A ILE* 3.7 33.2 - - + +
119A PHE* 3.9 17.5 - - + +
120A THR* 4.8 0.9 - - + -
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Residues in contact with GLY 101 (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 TYR* 5.8 0.4 - - - -
96A ASN 3.1 14.8 + - - -
97A SER* 3.4 12.1 + - - -
99A TYR 3.3 0.4 - - - -
100A LEU* 1.3 78.1 - - - +
102A PRO* 1.3 67.1 - - - +
104A LEU* 3.6 8.2 - - - +
105A LYS* 3.2 21.3 + - - +
246A MET* 4.0 18.6 - - - +
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Residues in contact with PRO 102 (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 SER 3.6 7.4 - - - +
98A LEU 3.1 28.9 - - - +
99A TYR 3.2 9.4 - - - +
101A GLY* 1.3 85.2 - - - +
103A ILE* 1.3 58.0 + - + +
105A LYS* 4.6 0.4 - - + -
106A PHE* 2.8 42.8 + - + +
128A PHE* 5.1 1.1 - - + -
172A VAL* 4.4 15.9 - - + -
230A LEU* 4.1 7.3 - - + +
239A ILE* 4.0 16.2 - - + -
243A THR* 3.2 27.5 - - + +
246A MET* 4.9 1.1 - - + -
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Residues in contact with ILE 103 (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 TYR* 3.4 47.1 - - + +
100A LEU 3.3 1.2 + - - +
102A PRO* 1.3 75.2 - - - +
104A LEU* 1.3 59.8 + - - +
107A GLY* 2.8 33.3 + - - +
111A GLN* 4.1 26.9 - - + +
112A LYS* 4.0 5.0 - - - +
115A TRP* 3.8 11.2 - - + -
116A ILE* 3.4 30.1 - - + -
172A VAL* 4.4 4.5 - - + -
190A LEU* 3.7 31.0 - - + -
230A LEU* 4.2 6.5 - - + -
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Residues in contact with LEU 104 (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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59A ASP* 4.3 30.5 - - + +
60A VAL* 4.4 20.0 - - + -
61A PRO* 4.0 22.0 - - + -
64A LEU* 5.4 5.8 - - + -
100A LEU 2.9 18.1 + - - +
101A GLY* 3.6 8.5 - - - +
103A ILE* 1.3 79.2 - - - +
105A LYS* 1.3 59.3 + - + +
112A LYS* 3.4 38.8 + - + +
116A ILE* 4.2 9.8 - - + +
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Residues in contact with LYS 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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101A GLY 3.2 16.9 + - - +
102A PRO* 4.0 2.2 - - + +
104A LEU* 1.3 80.8 - - + +
106A PHE* 1.3 90.8 + - + +
107A GLY 5.1 0.8 - - - +
112A LYS* 5.8 0.2 - - - -
242A GLN* 3.7 29.0 + - + +
246A MET* 4.9 17.8 - - + +
317A PHE* 5.8 6.9 - - - -
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Residues in contact with PHE 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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102A PRO* 2.8 33.0 + - + +
105A LYS* 1.3 99.6 - - + +
107A GLY* 1.3 64.8 + - - +
108A SER 3.9 0.2 + - - -
111A GLN* 4.6 0.3 - - - +
230A LEU* 4.0 16.0 - - + +
231A GLY* 4.3 14.7 + - - -
235A MET* 3.6 29.8 - - + -
238A LYS* 5.6 1.1 - - + -
239A ILE* 3.7 47.3 - - + -
242A GLN* 2.9 35.4 - - + -
243A THR* 4.6 1.8 - - - -
246A MET* 6.0 0.9 - - + -
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Residues in contact with GLY 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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103A ILE* 2.8 25.6 + - - -
104A LEU 5.1 0.2 - - - +
105A LYS 3.8 0.5 - - - -
106A PHE* 1.3 78.0 - - - +
108A SER* 1.3 65.2 + - - -
111A GLN* 3.3 17.3 - - - -
112A LYS* 3.5 15.2 - - - -
230A LEU* 3.5 10.9 - - - +
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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