Contacts of the helix formed by residues 108 - 128 (chain D) in PDB entry 4J4L
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 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.5 4.4 - - - +
42D GLU* 4.3 17.0 - - - +
105D PHE* 3.3 22.5 + - - +
107D SER* 1.3 85.8 + - - +
109D GLU* 1.3 66.4 + - - +
110D GLU 3.3 2.4 + - - -
111D GLN* 3.4 16.1 + - - +
112D ALA* 3.2 20.1 + - - +
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Residues in contact with GLU 109 (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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102D GLN* 4.5 10.0 + - - +
105D PHE 3.3 11.8 + - - +
106D GLU 5.0 2.4 - - - +
107D SER 3.9 1.6 - - - -
108D SER* 1.3 75.6 - - - +
110D GLU* 1.3 76.7 + - + +
112D ALA* 3.2 6.0 + - - +
113D ARG* 2.9 49.2 + - - +
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Residues in contact with GLU 110 (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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227B GLN* 5.7 3.3 + - - +
108D SER 3.3 0.8 - - - -
109D GLU* 1.3 93.5 - - + +
111D GLN* 1.3 57.9 - - - +
113D ARG* 3.3 10.0 + - - +
114D ALA* 2.9 31.2 + - - +
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Residues in contact with GLN 111 (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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31D TYR* 5.6 5.5 + - - -
34D ASP 5.1 0.2 - - - +
35D GLY* 3.2 35.8 - - - +
38D ALA* 4.1 17.7 - - + +
39D LEU* 3.7 18.8 - - + -
108D SER* 3.4 16.2 + - - +
109D GLU 3.3 0.4 - - - -
110D GLU* 1.3 77.6 - - - +
112D ALA* 1.3 62.7 + - - +
114D ALA* 3.2 13.4 + - - +
115D VAL* 3.1 19.5 + - - +
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Residues in contact with ALA 112 (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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39D LEU* 3.8 14.6 - - + +
101D LEU* 4.3 7.9 - - + +
102D GLN* 2.9 29.9 - - - +
105D PHE* 4.1 25.6 - - + -
108D SER 3.2 10.3 + - - +
109D GLU* 3.5 9.4 - - - +
111D GLN* 1.3 80.5 - - - +
113D ARG* 1.3 59.9 + - - +
115D VAL* 3.3 11.3 + - - +
116D GLN* 3.3 6.9 + - - +
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Residues in contact with ARG 113 (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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225B GLN* 4.9 13.1 - - - +
249B ASP* 3.0 52.3 + - - +
286B LYS* 5.4 8.3 - - - +
102D GLN* 3.5 16.3 - - - +
109D GLU* 2.9 31.9 + - - +
110D GLU* 3.5 15.3 - - - +
112D ALA* 1.3 73.4 - - - +
114D ALA* 1.3 59.3 + - - +
116D GLN* 3.1 11.8 + - - +
117D MET* 2.9 33.7 + - + +
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Residues in contact with ALA 114 (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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225B GLN* 3.7 24.0 - - - +
31D TYR* 4.6 14.5 - - + +
110D GLU 2.9 17.6 + - - +
111D GLN* 3.2 16.1 + - - +
113D ARG* 1.3 77.2 - - - +
115D VAL* 1.3 58.7 + - - +
117D MET* 4.3 4.3 - - - -
118D SER* 2.7 37.4 + - - +
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Residues in contact with VAL 115 (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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32D ILE* 4.1 14.3 - - + +
35D GLY* 3.7 36.1 - - - -
36D ILE* 3.9 8.1 - - + +
39D LEU* 3.9 16.8 - - + -
98D LEU* 4.7 10.1 - - + -
101D LEU* 5.6 3.8 - - + -
111D GLN* 3.1 18.9 + - - +
112D ALA 3.3 6.3 + - - +
113D ARG 3.3 0.4 - - - -
114D ALA* 1.3 77.0 - - - +
116D GLN* 1.3 60.5 + - - +
118D SER* 4.1 3.8 - - - -
119D THR* 2.6 34.1 + - - -
167D LEU* 6.0 0.2 - - + -
170D PHE* 4.1 25.1 - - + -
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Residues in contact with GLN 116 (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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95D GLU* 4.7 3.2 - - + +
98D LEU* 4.2 23.8 - - + +
99D GLU* 3.0 36.4 + - - +
102D GLN* 3.4 38.8 - - - +
112D ALA 3.3 1.2 + - - +
113D ARG* 3.1 13.4 + - - +
115D VAL* 1.3 79.4 - - - +
117D MET* 1.3 63.7 - - - +
119D THR* 3.5 3.5 + - - -
120D LYS* 3.4 40.6 + - - +
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Residues in contact with MET 117 (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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201B TYR* 4.1 12.3 - - + +
224B TYR* 3.9 12.8 - - + -
225B GLN* 3.0 46.2 - - + +
248B HIS* 3.5 19.1 - - + +
249B ASP* 2.9 30.3 - - - +
276B SER* 3.9 16.6 - - - +
113D ARG* 2.9 25.3 + - - +
114D ALA* 4.0 3.1 - - - +
116D GLN* 1.3 70.8 - - - +
118D SER* 1.3 67.0 + - - +
120D LYS* 2.9 22.2 + - - +
121D VAL* 3.1 13.1 + - - +
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Residues in contact with SER 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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201B TYR* 2.8 33.3 + - - -
28D GLN* 3.2 12.8 - - - +
31D TYR* 3.6 16.5 - - - -
32D ILE* 3.8 21.9 - - - +
114D ALA* 2.7 25.9 + - - -
115D VAL* 4.1 1.6 - - - -
117D MET* 1.3 73.4 - - - +
119D THR* 1.3 56.5 + - - +
121D VAL* 3.2 1.5 + - - -
122D LEU* 3.0 27.4 + - - +
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Residues in contact with THR 119 (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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32D ILE* 3.8 15.7 - - + +
91D LEU* 4.6 18.4 - - + +
95D GLU* 4.7 4.5 - - + -
98D LEU* 3.8 19.2 - - + +
115D VAL 2.6 22.9 + - - -
116D GLN 3.7 5.6 - - - -
117D MET 3.1 1.0 - - - -
118D SER* 1.3 75.3 - - - +
120D LYS* 1.3 61.4 + - - +
122D LEU* 3.7 2.8 - - + +
123D ILE* 3.1 41.5 + - + +
170D PHE* 3.6 26.5 - - + -
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Residues in contact with LYS 120 (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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276B SER* 3.4 35.4 - - - +
277B ALA* 4.4 17.1 - - + +
95D GLU* 2.7 49.6 + - - +
116D GLN* 3.4 31.5 + - - +
117D MET* 2.9 12.9 + - - +
119D THR* 1.3 77.6 - - - +
121D VAL* 1.3 64.3 + - - +
123D ILE* 3.4 7.7 + - - +
124D GLN* 3.3 15.6 + - - +
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Residues in contact with VAL 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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201B TYR* 4.3 3.8 - - - +
222B ARG* 4.6 6.1 - - - +
224B TYR* 3.4 40.2 - - + +
246B TRP* 6.3 0.7 - - + -
276B SER* 3.8 25.1 - - - +
28D GLN* 3.5 17.3 - - - +
117D MET* 3.1 12.9 + - - +
118D SER 3.2 7.6 + - - +
120D LYS* 1.3 71.9 - - - +
122D LEU* 1.3 64.1 + - - +
124D GLN* 2.9 17.6 + - - +
125D PHE* 3.0 37.3 + - + -
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Residues in contact with LEU 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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25D ILE* 4.1 15.3 - - + -
28D GLN* 3.9 13.8 - - + +
29D ILE* 3.7 32.5 - - + -
32D ILE* 3.7 21.5 - - + -
91D LEU* 3.9 26.7 - - + -
118D SER 3.0 16.3 + - - +
119D THR* 3.7 4.9 - - - +
121D VAL* 1.3 76.9 - - - +
123D ILE* 1.3 63.5 + - - +
125D PHE* 3.1 15.8 + - + +
126D LEU* 2.9 36.0 + - + +
174D LEU* 4.3 9.2 - - + -
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Residues in contact with ILE 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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88D ILE* 4.7 8.3 - - + +
91D LEU* 3.8 42.0 - - + +
92D LEU* 4.1 16.2 - - + +
95D GLU* 3.8 32.5 - - - +
119D THR* 3.1 22.4 + - + +
120D LYS* 3.7 7.6 - - - +
121D VAL 3.3 0.2 - - - -
122D LEU* 1.3 79.9 - - - +
124D GLN* 1.3 58.5 + - + +
126D LEU* 3.4 6.9 + - - +
127D GLN* 3.0 49.2 + - + +
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Residues in contact with GLN 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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222B ARG* 5.8 3.8 + - - +
246B TRP* 5.7 4.1 - - + -
276B SER 4.1 4.9 - - - +
277B ALA* 3.1 38.0 + - - +
278B GLY* 3.6 20.1 + - - +
120D LYS 3.3 4.7 + - - +
121D VAL* 2.9 11.3 + - + +
123D ILE* 1.3 76.9 - - + +
125D PHE* 1.3 68.2 + - + +
127D GLN* 3.2 27.8 + - - +
128D LYS* 3.4 39.0 + - - +
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Residues in contact with PHE 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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222B ARG* 3.7 30.1 - - - -
224B TYR* 5.3 1.3 - - - -
24D ARG* 3.6 46.4 - - + -
25D ILE* 3.7 31.9 - - + +
28D GLN* 3.8 23.6 - - + -
121D VAL* 3.0 34.7 + - + -
122D LEU* 3.4 19.1 - - - +
124D GLN* 1.3 76.4 - - + +
126D LEU* 1.3 62.8 + - - +
128D LYS* 3.2 22.0 + - - +
129D LYS* 3.8 9.5 + - - +
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Residues in contact with LEU 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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25D ILE* 4.1 19.7 - - + -
29D ILE* 6.1 0.2 - - + -
84D LEU* 3.9 19.8 - - + +
87D ILE* 3.3 34.5 - - + -
88D ILE* 3.8 23.4 - - + +
91D LEU* 3.9 18.8 - - + -
122D LEU* 2.9 26.1 + - + +
123D ILE* 3.8 4.3 - - - +
125D PHE* 1.3 76.2 - - - +
127D GLN* 1.3 62.5 + - - +
129D LYS* 3.1 18.8 + - + +
130D ALA* 3.5 7.8 + - - +
181D LEU* 4.0 24.9 - - + -
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Residues in contact with GLN 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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277B ALA 5.1 2.2 + - - -
88D ILE* 4.0 30.6 - - + +
92D LEU* 4.9 6.6 - - - +
123D ILE* 3.0 37.1 + - - +
124D GLN* 3.2 27.8 + - - +
126D LEU* 1.3 77.7 - - - +
128D LYS* 1.3 64.8 + - + +
129D LYS 3.2 0.7 + - - -
130D ALA* 3.7 7.9 + - - +
133D LEU* 3.7 32.2 - - + +
136D ILE* 4.5 10.7 - - + +
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Residues in contact with LYS 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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244B TYR* 5.5 8.9 + - - -
124D GLN* 3.4 35.5 + - - +
125D PHE* 3.2 12.8 + - - +
127D GLN* 1.3 81.0 - - - +
129D LYS* 1.3 60.0 + - + +
130D ALA 3.5 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