Contacts of the helix formed by residues 100 - 120 (chain P) in PDB entry 1JVP
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 PRO 100 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90P PHE* 5.6 2.2 - - + -
94P SER* 6.1 0.4 - - - -
97P THR* 5.8 4.3 - - + -
98P GLY 3.5 6.2 - - - +
99P ILE* 1.3 94.1 - - + +
101P LEU* 1.3 65.7 + - - +
102P PRO* 4.0 11.2 - - + -
103P LEU* 2.9 29.7 + - + +
104P ILE* 3.0 10.4 + - - -
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Residues in contact with LEU 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P ILE 3.4 3.7 + - - -
100P PRO* 1.3 69.5 - - - +
102P PRO* 1.3 69.3 - - + +
104P ILE* 3.0 19.5 + - + -
105P LYS* 2.8 42.2 + - + +
197P VAL* 5.5 5.8 - - + -
256P ASP* 4.4 15.9 - - - +
285P PHE* 4.1 25.1 - - + -
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Residues in contact with PRO 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100P PRO* 3.4 12.6 - - + -
101P LEU* 1.3 99.5 - - + +
103P LEU* 1.3 54.8 + - - +
105P LYS* 3.7 8.7 - - + +
106P SER* 2.9 27.9 + - - -
290P THR* 4.3 14.7 + - - +
292P PRO* 3.7 17.7 - - + +
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Residues in contact with LEU 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P PHE* 3.7 32.1 - - + -
99P ILE* 3.7 14.6 - - + -
100P PRO* 2.9 23.9 + - + +
102P PRO* 1.3 76.4 - - - +
104P ILE* 1.3 67.7 + - - +
106P SER* 3.2 3.1 + - - +
107P TYR* 2.9 52.1 + - + +
139P GLY 5.1 0.2 - - - +
292P PRO* 3.7 37.8 - - + +
293P VAL 5.0 1.6 - - - +
294P PRO* 3.8 19.5 - - + -
295P HIS 5.2 0.2 - - - +
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Residues in contact with ILE 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P ILE* 3.4 34.5 - - + +
100P PRO 3.0 14.6 + - - +
101P LEU* 3.4 16.6 - - + +
103P LEU* 1.3 76.5 - - - +
105P LYS* 1.3 57.1 + - - +
107P TYR* 3.3 2.1 + - - +
108P LEU* 2.9 28.6 + - - +
193P PHE* 3.9 33.4 - - + -
196P MET* 3.5 52.0 - - + +
197P VAL* 3.9 13.2 - - + +
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Residues in contact with LYS 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P LEU* 2.8 35.1 + - - +
102P PRO* 3.7 8.5 - - + +
104P ILE* 1.3 73.1 - - - +
106P SER* 1.3 62.1 + - - +
108P LEU* 3.3 3.5 + - - +
109P PHE* 2.9 25.5 + - - +
256P ASP* 5.1 2.6 + - - -
285P PHE* 3.1 67.2 + - + +
286P PHE* 3.7 12.6 - - + -
288P ASP* 2.6 35.6 + - - +
289P VAL* 4.1 17.9 - - + -
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Residues in contact with SER 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P PRO 2.9 16.0 + - - -
103P LEU* 3.5 8.2 - - - +
105P LYS* 1.3 76.0 - - - +
107P TYR* 1.3 62.8 + - - +
109P PHE* 3.3 2.8 + - - +
110P GLN* 3.0 45.7 + - - +
139P GLY 4.4 1.9 + - - -
289P VAL* 4.0 7.8 - - - +
290P THR 3.2 27.2 + - - -
291P LYS* 3.8 11.4 - - - +
292P PRO* 3.7 9.7 - - - +
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Residues in contact with TYR 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P LEU* 4.2 9.4 - - + -
90P PHE* 4.0 18.3 - + - -
99P ILE* 5.2 1.6 - - + -
103P LEU* 2.9 43.7 + - + +
104P ILE* 3.7 4.7 - - - +
106P SER* 1.3 76.6 - - - +
108P LEU* 1.3 63.2 + - - +
110P GLN* 3.4 2.3 + - - -
111P LEU* 3.0 31.2 + - + +
135P ILE* 3.7 27.9 - - + +
136P ASN 5.0 0.2 + - - -
139P GLY 3.6 25.8 - - - -
140P ALA 4.2 1.5 + - - -
141P ILE* 3.6 41.2 - - + +
196P MET* 4.4 16.2 - - + -
294P PRO* 3.5 30.0 - - - +
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Residues in contact with LEU 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P ILE 2.9 17.8 + - - +
105P LYS* 3.7 5.2 - - - +
107P TYR* 1.3 77.4 - - - +
109P PHE* 1.3 62.8 + - - +
111P LEU* 3.4 4.6 + - - +
112P LEU* 3.0 31.9 + - + +
189P LEU* 3.7 35.2 - - + -
193P PHE* 3.6 57.4 - - + -
196P MET* 4.9 5.5 - - + +
262P LEU* 3.8 9.0 - - + -
266P MET* 4.4 7.0 - - + -
285P PHE* 4.2 2.0 - - + -
286P PHE* 3.7 22.2 - - + -
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Residues in contact with PHE 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P LYS 2.9 17.1 + - - +
106P SER 3.5 4.7 - - - +
108P LEU* 1.3 76.5 - - - +
110P GLN* 1.3 65.2 + - + +
112P LEU* 3.3 5.9 + - - +
113P GLN* 3.0 54.4 + - + +
281P LEU* 3.5 43.0 - - + +
286P PHE* 3.6 35.6 - + + -
289P VAL* 4.0 28.7 - - + -
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Residues in contact with GLN 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62P ASN* 3.2 31.8 + - - +
106P SER* 3.0 37.2 + - - +
107P TYR* 4.1 4.9 - - - -
109P PHE* 1.3 77.4 - - + +
111P LEU* 1.3 61.0 + - - +
113P GLN* 3.1 18.6 + - - +
114P GLY 3.0 22.9 + - - -
139P GLY 3.0 23.8 + - - -
140P ALA* 3.3 9.4 - - - +
141P ILE* 3.1 28.9 + - + -
291P LYS* 4.5 10.9 + - - +
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Residues in contact with LEU 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62P ASN* 5.1 0.9 - - - +
87P LEU* 5.5 1.6 - - + -
107P TYR* 3.0 24.8 + - + +
108P LEU* 3.8 4.7 - - - +
110P GLN* 1.3 75.8 - - - +
112P LEU* 1.3 57.0 + - - +
114P GLY* 3.2 2.9 + - - +
115P LEU* 2.9 32.6 + - - +
133P LEU* 3.7 32.8 - - + -
141P ILE* 3.8 32.8 - - + +
142P LYS 4.3 0.7 - - - -
143P LEU* 3.9 32.5 - - + +
189P LEU* 3.6 33.9 - - + -
196P MET* 5.6 3.8 - - + -
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Residues in contact with LEU 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P LEU* 3.0 28.6 + - + +
109P PHE 3.6 5.2 - - - +
110P GLN 3.2 0.2 - - - -
111P LEU* 1.3 74.3 - - - +
113P GLN* 1.3 60.7 + - - +
115P LEU* 4.4 2.9 - - + -
116P ALA* 2.9 30.7 + - - +
186P ILE* 4.1 12.3 - - + -
189P LEU* 3.6 21.8 - - + -
262P LEU* 5.0 1.6 - - + -
266P MET* 4.2 7.4 - - + -
277P ALA* 3.5 16.9 - - + +
280P ALA* 3.7 28.0 - - + -
281P LEU* 3.6 14.9 - - + +
286P PHE* 3.6 33.0 - - + -
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Residues in contact with GLN 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P HIS* 3.9 14.0 + - + +
62P ASN* 4.0 12.8 + - - +
109P PHE* 3.0 46.2 + - + +
110P GLN* 3.1 17.1 + - - +
112P LEU* 1.3 75.2 - - - +
114P GLY* 1.3 64.1 + - - +
116P ALA* 3.4 2.9 + - - +
117P PHE* 3.1 23.6 + - - +
281P LEU* 3.8 23.3 - - + -
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Residues in contact with GLY 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P HIS* 4.0 9.8 - - - -
62P ASN* 4.0 14.1 - - - -
110P GLN 3.0 13.8 + - - -
111P LEU 3.2 3.3 + - - -
113P GLN* 1.3 77.6 - - - +
115P LEU* 1.3 61.0 + - - +
117P PHE* 3.3 5.9 + - - +
118P CYS* 3.1 19.4 + - - -
143P LEU* 3.7 19.5 - - - +
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Residues in contact with LEU 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P LEU 2.9 16.5 + - - +
112P LEU* 3.8 4.7 - - + +
114P GLY* 1.3 74.6 - - - +
116P ALA* 1.3 56.9 + - - +
118P CYS* 4.5 0.7 - - - +
119P HIS* 2.7 60.6 + - + +
125P HIS* 5.7 2.2 - - - +
143P LEU* 3.9 23.1 - - + +
185P ASP* 4.0 36.1 - - + +
186P ILE* 4.1 13.5 - - + -
189P LEU* 3.8 26.9 - - + -
277P ALA* 3.9 8.7 - - + -
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Residues in contact with ALA 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P LEU 2.9 19.3 + - - +
113P GLN* 3.7 4.7 - - - +
115P LEU* 1.3 75.1 - - - +
117P PHE* 1.3 56.5 + - - +
119P HIS* 3.9 3.6 - - - +
120P SER* 3.0 30.8 + - - -
277P ALA* 3.5 15.1 - - + +
278P LYS* 4.1 29.1 + - + +
281P LEU* 4.2 13.5 - - + -
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Residues in contact with PHE 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P GLU 5.4 1.3 - - - -
58P LEU* 3.7 30.7 - - + -
59P ASN 3.5 30.3 - - - -
60P HIS* 3.4 39.7 - + + +
113P GLN 3.1 8.5 + - - +
114P GLY 3.4 9.0 - - - +
115P LEU 3.1 0.2 - - - -
116P ALA* 1.3 74.3 - - - +
118P CYS* 1.3 69.8 + - - +
120P SER* 2.7 22.9 + - - -
121P HIS* 3.1 37.7 + + - -
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Residues in contact with CYS 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P LEU* 4.5 14.4 - - - -
114P GLY 3.1 10.5 + - - -
115P LEU* 3.9 1.3 - - - +
117P PHE* 1.3 86.8 - - - +
119P HIS* 1.3 58.9 + - - +
121P HIS* 2.9 18.0 + - - +
122P ARG 3.2 0.2 + - - -
123P VAL* 2.9 31.4 + - - -
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Residues in contact with HIS 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P LEU* 2.7 44.5 + - + +
116P ALA* 4.1 4.0 - - - +
118P CYS* 1.3 73.4 - - - +
120P SER* 1.3 58.4 + - - +
122P ARG* 2.9 36.5 + - - +
123P VAL 3.4 17.7 - - - +
124P LEU* 4.5 0.4 - - - -
182P THR* 3.3 51.0 + - + +
185P ASP* 2.8 34.0 + - + +
186P ILE* 4.6 7.7 - - + +
277P ALA* 4.5 8.9 + - + +
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Residues in contact with SER 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P ALA 3.0 18.3 + - - -
117P PHE* 2.7 21.0 + - - -
119P HIS* 1.3 74.7 - - - +
121P HIS* 1.3 70.0 + - - +
122P ARG* 3.4 14.6 + - - +
278P LYS* 6.4 1.8 - - - -
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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