Contacts of the helix formed by residues 98 - 113 (chain A) in PDB entry 3JCA
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 ALA 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLY* 5.8 0.2 - - - -
97A GLU* 1.3 81.0 - - - +
99A THR* 1.3 67.4 + - - +
100A LYS* 4.0 21.3 - - + -
101A ASP* 2.8 27.4 + - - +
102A VAL* 3.0 11.2 + - - +
126A ALA* 6.0 0.2 - - - -
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Residues in contact with THR 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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97A GLU 3.9 0.4 + - - -
98A ALA* 1.3 72.0 - - - +
100A LYS* 1.3 58.3 + - - +
102A VAL* 3.2 10.5 + - - +
103A LEU* 2.8 49.1 + - + +
126A ALA* 5.5 2.9 + - - +
129A SER* 4.7 6.2 + - - -
131A SER* 3.4 32.9 + - - +
132A ILE* 4.0 13.4 - - + +
178B TYR* 4.5 10.5 - - - +
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Residues in contact with LYS 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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94A ARG* 4.6 6.5 + - - +
98A ALA* 4.0 18.6 - - + -
99A THR* 1.3 76.3 - - - +
101A ASP* 1.3 72.2 + - - +
103A LEU* 3.7 8.5 - - - -
104A GLN* 2.8 22.3 + - - +
178B TYR* 3.5 54.2 - - + -
179B THR* 6.4 0.7 - - + -
182B HIS* 2.9 14.3 + - + +
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Residues in contact with ASP 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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79A HIS* 3.7 9.5 - - - +
94A ARG* 2.9 49.1 + - - +
95A THR* 4.4 4.1 + - - -
96A GLY* 3.3 34.3 + - - +
98A ALA* 2.8 39.8 + - - +
100A LYS* 1.3 78.1 - - - +
102A VAL* 1.3 65.1 + - - +
104A GLN* 3.6 1.9 - - - +
105A HIS* 3.2 23.0 + - - +
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Residues in contact with VAL 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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64A MET* 4.1 14.0 - - + +
79A HIS* 3.8 23.3 - - + +
97A GLU 4.4 1.1 - - - +
98A ALA 3.0 12.5 + - - +
99A THR* 3.4 8.5 - - - +
101A ASP* 1.3 76.7 - - - +
103A LEU* 1.3 56.5 + - - +
105A HIS* 3.3 5.0 + - - +
106A LEU* 2.9 48.5 + - + +
126A ALA* 3.9 29.2 - - + +
127A TYR* 4.2 15.7 - - + -
132A ILE* 4.1 17.3 - - + -
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Residues in contact with LEU 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 THR* 2.8 39.7 + - + +
100A LYS* 3.9 4.9 - - - +
102A VAL* 1.3 73.4 - - - +
104A GLN* 1.3 60.3 + - - +
106A LEU* 3.5 12.1 - - + +
107A ALA* 2.8 31.7 + - - +
131A SER 5.6 1.8 - - - +
132A ILE* 4.9 7.4 - - + -
135A PHE* 3.5 45.4 - - + -
178B TYR* 3.7 24.7 - - + +
182B HIS* 3.9 11.6 - - + -
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Residues in contact with GLN 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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94A ARG* 3.5 36.0 + - - +
100A LYS 2.8 20.2 + - - +
101A ASP 3.6 6.3 - - - +
102A VAL 3.3 0.4 - - - -
103A LEU* 1.3 75.4 - - - +
105A HIS* 1.3 64.8 + - - +
107A ALA* 3.3 2.3 + - - +
108A GLN* 3.0 57.3 + - - +
179B THR* 3.2 13.0 + - - +
181B HIS* 3.7 32.1 + - - +
182B HIS* 3.2 27.9 + - - +
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Residues in contact with HIS 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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64A MET* 3.6 20.4 - - + -
79A HIS* 3.0 42.0 + - + -
80A VAL 3.8 0.4 - - - -
81A THR* 2.8 33.7 + - - -
90A PHE* 3.3 35.0 - + - -
92A THR* 2.8 25.1 + - + +
101A ASP 3.2 6.7 + - - +
102A VAL 3.5 7.0 - - - +
104A GLN* 1.3 81.1 - - - +
106A LEU* 1.3 60.5 + - + +
108A GLN* 3.2 11.1 + - - +
109A SER* 2.8 27.9 + - - -
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Residues in contact with LEU 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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62A TRP* 6.1 2.2 - - + -
64A MET* 4.2 20.4 - - - -
81A THR* 5.1 1.3 - - + +
102A VAL* 2.9 40.0 + - + +
103A LEU* 3.5 16.8 - - + +
104A GLN 3.2 0.2 - - - -
105A HIS* 1.3 77.4 - - + +
107A ALA* 1.3 53.8 + - - +
109A SER* 2.6 27.8 + - - +
110A PHE* 2.8 42.6 + - + -
119A ILE* 4.8 13.0 - - + -
132A ILE* 5.4 6.1 - - + -
135A PHE* 4.0 25.1 - - + -
136A LEU* 6.5 0.4 - - + -
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Residues in contact with ALA 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 LEU 2.8 19.8 + - - +
104A GLN* 3.6 4.5 - - - +
106A LEU* 1.3 72.4 - - - +
108A GLN* 1.3 62.6 + - - +
110A PHE* 3.2 20.1 + - - +
111A ALA* 3.2 9.9 + - - +
135A PHE* 5.6 2.4 - - + -
139A TRP* 6.1 1.3 - - - -
182B HIS* 4.3 20.6 - - + +
185B ALA* 3.9 27.5 - - + +
186B HIS* 4.7 6.9 - - + +
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Residues in contact with GLN 108 (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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90A PHE* 3.7 16.4 - - + -
92A THR* 2.6 41.7 + - - +
94A ARG* 5.7 0.4 - - - +
104A GLN* 3.0 40.4 + - - +
105A HIS* 3.4 5.2 - - - +
107A ALA* 1.3 77.4 - - - +
109A SER* 1.3 50.9 + - - +
111A ALA* 3.2 3.9 + - - +
112A TYR* 2.7 34.5 + - - +
112B TYR* 3.5 16.0 + - - +
181B HIS* 5.4 4.9 + - - +
185B ALA* 4.4 10.5 - - + -
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Residues in contact with SER 109 (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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62A TRP* 3.9 13.7 - - - -
81A THR* 4.7 2.5 + - - -
90A PHE* 3.5 22.4 - - - -
105A HIS* 2.8 24.4 + - - -
106A LEU* 2.6 29.0 + - - +
108A GLN* 1.3 70.0 - - - +
110A PHE* 1.3 63.1 + - - +
112A TYR* 4.0 2.7 - - - -
113A MET* 2.7 41.6 + - - +
114A GLY 3.1 5.2 + - - -
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Residues in contact with PHE 110 (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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62A TRP* 5.0 3.6 - + - -
106A LEU* 2.8 44.9 + - + -
107A ALA* 3.2 11.4 + - - +
109A SER* 1.3 78.8 + - - +
111A ALA* 1.3 61.1 + - - +
114A GLY* 2.9 46.1 + - - +
115A ILE* 3.9 20.9 - - + -
116A PRO* 4.4 4.0 - - + -
135A PHE* 3.5 34.1 - + - -
139A TRP* 3.5 38.6 - + + -
141A ILE* 3.9 16.2 - - + -
189B PHE* 3.1 33.3 - + + -
193B HIS* 3.6 1.0 - - - -
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Residues in contact with ALA 111 (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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107A ALA 3.2 11.9 + - - +
108A GLN* 3.5 8.5 - - - +
110A PHE* 1.3 78.7 - - - +
112A TYR* 1.3 59.2 + - - +
88B PHE* 5.1 5.7 - - - -
112B TYR* 3.9 17.7 - - + -
185B ALA* 4.0 19.1 - - + +
188B LEU* 4.7 10.8 - - + -
189B PHE* 4.0 9.3 - - - +
193B HIS* 2.7 29.7 + - - -
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Residues in contact with TYR 112 (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 PHE* 3.5 31.1 - + - -
89A THR 3.2 21.8 + - - -
90A PHE* 3.4 42.4 - + + -
108A GLN 2.7 20.5 + - - +
109A SER* 4.0 4.0 - - - -
111A ALA* 1.3 76.2 - - - +
113A MET* 1.3 60.9 + - + +
188A LEU* 3.7 19.8 + - + +
192A ASN* 2.9 18.4 + - - +
111B ALA* 3.2 40.3 + - + -
112B TYR* 3.6 31.2 - + + +
208B TRP* 4.8 9.9 - - - -
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Residues in contact with MET 113 (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 ARG* 3.2 14.2 + - - -
62A TRP* 3.4 36.1 - - + -
81A THR* 3.7 30.5 - - + +
82A VAL 3.8 4.3 - - - -
83A ASP* 3.3 35.4 - - + +
88A PHE* 3.6 25.6 - - + +
90A PHE* 4.0 9.2 - - + -
109A SER* 2.7 18.9 + - - +
110A PHE 4.0 0.2 - - - -
112A TYR* 1.3 94.0 - - + +
114A GLY* 1.3 56.9 + - - +
207A HIS* 2.9 21.8 + - + +
193B HIS* 4.6 1.6 - - - -
208B TRP* 4.3 2.3 - - - -
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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