Contacts of the helix formed by residues 117 - 132 (chain D) 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 SER 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D GLU* 4.3 3.8 + - - -
61D GLU* 2.7 26.9 + - - +
105D ILE* 4.4 0.2 - - - +
106D GLU* 3.7 6.9 - - - +
116D ALA* 1.3 79.1 - - - +
118D PHE* 1.3 64.3 + - - +
120D SER* 3.1 31.4 + - - -
121D THR 3.5 4.0 + - - -
358D GLU* 3.2 15.3 - - - -
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Residues in contact with PHE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLU* 3.5 34.5 + - - +
117D SER* 1.3 70.8 - - - +
119D LEU* 1.3 64.3 + - - +
121D THR* 3.0 15.9 + - + -
122D VAL* 3.1 32.9 + - + +
144D THR* 4.9 16.4 - - + -
148D THR* 6.1 1.1 - - - -
292D GLU* 4.0 31.0 - - + -
295D ILE* 4.0 8.7 - - + -
296D GLY* 5.1 2.2 - - - -
354D ALA* 3.7 30.3 - - + -
357D LEU* 3.8 41.1 - - + -
358D GLU* 3.2 14.0 + - + +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D PHE* 4.0 7.6 - - + -
61D GLU* 3.5 31.0 - - - +
118D PHE* 1.3 77.2 - - - +
120D SER* 1.3 57.2 + - - +
122D VAL* 3.2 12.3 + - + -
123D LEU* 2.9 38.2 + - + +
351D TYR* 4.2 24.7 - - + +
354D ALA* 4.0 21.8 - - + -
355D ARG* 3.6 41.7 - - + +
358D GLU* 2.9 19.1 + - - +
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Residues in contact with SER 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLU* 4.8 1.0 + - - -
61D GLU* 3.2 25.7 + - - +
64D ILE* 3.8 14.1 - - - +
105D ILE* 4.0 5.4 - - - -
116D ALA* 3.7 22.7 - - - +
117D SER* 3.1 25.7 + - - -
118D PHE 3.2 0.2 - - - -
119D LEU* 1.3 75.9 - - - +
121D THR* 1.3 57.1 + - - +
123D LEU* 3.3 7.1 + - - +
124D VAL* 2.9 35.4 + - - +
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Residues in contact with THR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ILE* 3.4 22.9 - - + +
106D GLU* 3.0 34.4 + - - +
117D SER 3.5 0.6 + - - -
118D PHE* 3.0 14.8 + - + -
120D SER* 1.3 77.4 - - - +
122D VAL* 1.3 63.5 + - + +
124D VAL* 3.3 1.6 + - - +
125D ILE* 3.0 36.5 + - + +
143D ASN* 3.9 15.9 - - + +
144D THR* 3.8 29.4 - - + -
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Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D PHE* 3.1 42.4 + - + +
119D LEU* 3.4 12.6 - - + +
121D THR* 1.3 77.4 - - + +
123D LEU* 1.3 56.0 - - - +
125D ILE* 3.3 3.5 + - + -
126D GLU* 3.0 25.5 + - - +
295D ILE* 3.9 11.9 - - + +
296D GLY* 5.3 2.2 - - - +
299D ALA* 3.5 25.7 - - + +
350D THR* 3.9 17.0 - - + -
351D TYR* 4.2 20.4 - - + -
354D ALA* 3.9 11.0 - - + -
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D PHE* 3.6 37.2 - - + -
61D GLU* 4.0 35.7 - - + +
64D ILE* 6.3 0.2 - - + -
65D LYS* 4.7 24.4 - - + +
119D LEU* 2.9 26.6 + - + +
120D SER* 3.7 5.6 - - - +
122D VAL* 1.3 71.7 - - - +
124D VAL* 1.3 61.6 + - + +
126D GLU* 3.7 8.0 - - - +
127D GLU* 2.9 32.1 + - - +
351D TYR* 3.4 35.9 - - + +
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 3.5 29.2 - - + -
65D LYS* 6.0 0.7 - - - +
68D VAL* 3.9 14.1 - - + +
102D LEU* 3.9 16.6 - - + -
105D ILE* 3.7 28.7 - - + -
120D SER 2.9 22.3 + - - +
121D THR 3.7 4.9 - - - +
123D LEU* 1.3 71.9 - - - +
125D ILE* 1.3 61.6 + - - +
127D GLU* 3.3 4.6 + - - +
128D LEU* 2.9 48.0 + - + +
139D CYS* 3.9 6.3 - - - -
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Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D THR* 3.0 40.3 + - + +
122D VAL* 3.6 6.1 - - + +
124D VAL* 1.3 75.4 - - - +
126D GLU* 1.3 58.3 + - - +
128D LEU* 4.6 5.2 - - - -
129D ALA* 2.9 28.9 + - - +
136D ALA* 3.5 16.2 - - + +
139D CYS* 4.6 7.9 - - - -
140D GLU* 3.8 38.4 - - + +
144D THR* 3.9 5.8 - - + -
296D GLY* 3.5 29.4 - - - +
299D ALA* 4.1 1.1 - - + -
300D GLN* 3.6 20.4 - - + +
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LYS* 5.9 2.4 - - - -
122D VAL 3.0 16.3 + - - +
123D LEU* 3.7 10.9 - - - +
125D ILE* 1.3 77.0 - - - +
127D GLU* 1.3 64.0 + - - +
129D ALA 3.1 1.9 + - - -
130D LYS* 3.0 36.6 + - - +
299D ALA* 3.4 19.0 + - + +
302D LEU* 3.7 9.6 - - + -
303D GLY* 3.3 27.2 - - - +
347D ARG* 3.0 35.2 + - - -
351D TYR* 2.5 32.4 + - - -
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LYS* 3.5 43.7 - - + +
68D VAL* 3.8 10.3 - - + -
69D LYS* 3.6 40.3 - - - +
72D ALA* 4.6 3.0 - - - +
123D LEU 2.9 20.5 + - - +
124D VAL 3.7 3.4 - - - +
125D ILE 3.3 0.2 - - - -
126D GLU* 1.3 77.6 - - - +
128D LEU* 1.3 61.5 + - - +
130D LYS* 3.1 53.8 + - - +
131D VAL* 3.9 8.0 + - - +
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D VAL* 3.8 18.2 - - + -
71D PHE* 4.4 5.8 - - + -
72D ALA* 4.5 5.6 - - + -
76D ILE* 3.6 30.4 - - + +
97D LEU* 4.0 20.0 - - + -
102D LEU* 4.9 1.1 - - + -
124D VAL* 2.9 26.3 + - + +
125D ILE* 3.8 3.8 - - - +
127D GLU* 1.3 75.5 - - - +
129D ALA* 1.3 58.2 + - - +
131D VAL* 3.0 7.8 + - - +
132D ASP* 2.8 27.8 + - - +
135D VAL* 4.3 3.9 - - + +
136D ALA* 4.0 16.6 - - - +
139D CYS* 3.6 39.0 - - + -
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ILE 2.9 18.1 + - - +
126D GLU 3.1 5.3 + - - +
128D LEU* 1.3 72.1 - - - +
130D LYS* 1.3 64.4 + - - +
131D VAL 3.0 3.6 + - - -
132D ASP 3.6 10.6 + - - -
133D ALA* 3.8 6.4 + - - -
136D ALA* 3.6 17.0 - - + +
300D GLN* 3.2 34.8 - - + +
303D GLY 3.7 2.7 - - - -
304D LEU* 3.4 18.5 - - - +
403D TYR* 4.1 2.9 - - - -
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Residues in contact with LYS 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LYS* 4.6 11.1 - - - +
126D GLU* 3.0 41.0 + - - +
127D GLU* 3.1 42.9 + - - +
128D LEU 3.2 0.6 - - - -
129D ALA* 1.3 75.6 - - - +
131D VAL* 1.3 57.7 + - + +
303D GLY 3.2 21.3 + - - +
306D GLN* 4.2 18.5 - - + +
307D GLY* 3.7 14.8 - - - +
310D ASP* 4.9 7.8 + - - +
347D ARG* 5.2 1.2 - - - +
403D TYR* 2.7 29.2 + - - -
1438D EDO 4.3 0.5 - - - -
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Residues in contact with VAL 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ALA* 3.7 29.4 - - + +
73D GLN* 4.5 15.3 - - + +
76D ILE* 3.8 9.2 - - + -
77D ALA* 3.7 30.3 - - + +
80D VAL* 3.8 12.6 - - + +
127D GLU 4.5 4.5 - - - +
128D LEU 3.0 7.3 + - - +
129D ALA 3.9 1.3 - - - -
130D LYS* 1.3 82.9 - - + +
132D ASP* 1.3 60.1 + - - +
402D LYS* 4.9 0.7 + - - -
403D TYR* 4.2 4.5 + - - -
1438D EDO 3.1 38.7 + - - +
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ILE* 4.0 4.9 - - + -
80D VAL* 3.8 20.8 - - + +
83D MET* 3.5 26.2 - - - +
128D LEU 2.8 18.4 + - - +
129D ALA* 3.6 1.0 + - - -
131D VAL* 1.3 76.0 - - - +
133D ALA* 1.3 63.5 + - - +
134D SER* 3.0 21.4 + - - -
135D VAL* 3.1 28.1 + - + +
136D ALA* 3.1 9.5 + - - +
257D ALA* 5.0 1.6 - - - +
402D LYS* 2.9 28.4 + - - +
403D TYR* 5.7 0.4 - - - -
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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
------------------------------------------------------------
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