Contacts of the helix formed by residues 102 - 118 (chain D) in PDB entry 4UNA
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 ASN 102 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLU* 3.3 25.4 + - - -
100D LEU 3.3 4.2 + - - +
101D PHE* 1.3 72.8 - - - +
103D MET* 1.3 66.7 + - - +
104D ARG* 3.1 10.3 + - - +
105D GLU* 2.8 44.7 + - - +
106D GLN* 2.9 24.0 + - - +
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Residues in contact with MET 103 (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 ASN* 1.3 75.0 - - - +
104D ARG* 1.3 64.6 + - + +
106D GLN* 3.3 16.0 + - - +
107D ILE* 3.2 41.9 + - + +
145D LEU* 3.9 28.7 - - + -
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Residues in contact with ARG 104 (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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5D GLU* 3.3 48.8 + - - +
6D ASN* 5.0 3.2 + - - +
8D SER* 5.8 0.7 - - - +
9D GLY* 5.5 1.6 - - - -
102D ASN* 3.1 9.0 + - - +
103D MET* 1.3 84.2 - - + +
105D GLU* 1.3 61.4 + - + +
107D ILE* 3.5 3.8 + - - +
108D ALA* 3.2 19.1 + - - +
182D LEU* 2.8 67.7 + - + +
183D ASN* 3.2 22.7 + - - +
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D SER* 3.9 38.2 - - - +
9D GLY* 5.0 0.7 - - - +
12D ALA* 3.4 12.7 - - + +
94D MET* 4.6 7.4 - - - +
100D LEU 4.4 1.0 - - - +
101D PHE* 3.3 30.3 - - + -
102D ASN* 2.8 54.2 + - - +
104D ARG* 1.3 73.4 - - + +
106D GLN* 1.3 60.0 + - - +
108D ALA* 3.4 1.2 + - - -
109D PHE* 2.8 32.4 + - - +
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Residues in contact with GLN 106 (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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99D ARG 5.5 0.6 + - - -
101D PHE* 2.7 27.9 + - + +
102D ASN* 2.9 21.9 + - - +
103D MET* 3.3 13.2 + - - +
105D GLU* 1.3 74.8 - - - +
107D ILE* 1.3 60.3 + - + +
109D PHE* 3.4 0.9 + - - +
110D ILE* 2.9 39.0 + - + +
141D TRP* 3.5 65.8 - - + +
144D ASN* 5.2 5.2 - - - +
145D LEU* 4.9 8.3 - - + +
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Residues in contact with ILE 107 (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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103D MET* 3.2 41.5 + - + +
104D ARG* 3.9 5.6 - - - +
105D GLU 3.3 0.2 - - - -
106D GLN* 1.3 75.0 - - - +
108D ALA* 1.3 55.4 + - - +
110D ILE* 3.7 2.6 - - - +
111D LYS* 2.8 36.9 + - - +
145D LEU* 4.2 23.6 - - + -
176D THR* 3.8 15.5 - - - +
177D ILE* 3.6 35.9 - - + +
180D SER* 3.8 22.0 - - - +
183D ASN* 4.0 5.2 - - - +
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Residues in contact with ALA 108 (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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9D GLY* 3.2 27.4 - - - +
12D ALA* 3.8 3.6 - - + -
13D TYR* 3.4 17.0 - - + +
104D ARG 3.2 11.6 + - - +
105D GLU 3.7 4.3 - - - +
107D ILE* 1.3 76.1 - - - +
109D PHE* 1.3 56.5 + - - +
111D LYS* 3.3 8.1 + - - +
112D GLY 2.9 24.3 + - - -
183D ASN* 3.3 28.4 + - + +
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Residues in contact with PHE 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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12D ALA 3.3 16.3 + - - +
15D LEU* 3.9 21.5 - - + -
16D GLY* 3.5 30.7 - - - -
19D ILE* 4.5 13.2 - - + -
95D LEU* 5.5 0.2 - - + -
98D ILE* 3.8 20.0 - - + -
101D PHE* 4.1 19.3 - + + -
105D GLU 2.8 21.2 + - - +
106D GLN 3.8 2.7 - - - +
108D ALA* 1.3 69.5 - - - +
110D ILE* 1.3 66.9 + - - +
112D GLY* 3.3 1.2 + - - -
113D LEU* 2.8 46.1 + - + +
134D LEU* 3.8 25.8 - - + -
138D VAL* 4.2 7.6 - - + -
141D TRP* 3.9 15.9 - + + -
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Residues in contact with ILE 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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106D GLN 2.9 25.5 + - - +
107D ILE* 3.8 3.6 - - - +
109D PHE* 1.3 77.6 - - + +
111D LYS* 1.3 58.9 + - - +
113D LEU* 3.4 5.0 + - - +
114D TYR* 2.9 28.6 + - - +
127D ILE* 4.9 8.0 - - + +
138D VAL* 3.8 30.1 - - + -
141D TRP* 4.0 26.7 - - + -
142D LEU* 3.7 23.3 - - + -
145D LEU* 4.5 9.0 - - + -
173D PHE* 4.2 18.6 - - + -
177D ILE* 3.9 17.5 - - + -
178D LEU* 6.0 0.2 - - + -
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Residues in contact with LYS 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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13D TYR* 3.9 6.3 - - + -
107D ILE* 2.8 18.3 + - - +
108D ALA* 3.3 14.1 - - - +
110D ILE* 1.3 76.8 - - - +
112D GLY* 1.3 55.7 + - - +
114D TYR* 3.1 4.9 + - - +
115D VAL* 3.0 30.7 + - - +
177D ILE* 3.2 18.6 - - - +
178D LEU* 3.3 30.0 + - + +
180D SER* 2.7 46.7 + - - +
183D ASN* 3.9 10.6 + - - -
184D PRO 3.4 17.4 + - - -
185D LEU* 4.6 0.6 - - - +
186D PRO* 3.5 26.5 - - + -
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Residues in contact with GLY 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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13D TYR* 3.6 34.2 - - - -
16D GLY 3.7 7.4 - - - -
17D LEU* 3.2 15.5 - - - +
108D ALA 2.9 10.7 + - - -
109D PHE 3.7 2.0 - - - -
111D LYS* 1.3 72.9 - - - +
113D LEU* 1.3 63.9 + - - +
115D VAL* 3.3 0.9 + - - -
116D ALA* 3.1 20.6 + - - +
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Residues in contact with LEU 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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16D GLY* 3.6 22.4 - - - +
19D ILE* 4.6 4.5 - - + -
20D GLY* 3.9 8.7 - - - +
109D PHE* 2.8 35.7 + - + +
110D ILE* 3.8 4.9 - - - +
112D GLY* 1.3 72.1 - - - -
114D TYR* 1.3 57.9 + - - +
116D ALA* 4.5 0.9 - - - -
117D GLU* 2.8 46.1 + - + +
127D ILE* 4.0 26.8 - - + +
129D ASN* 4.9 3.8 - - - +
134D LEU* 4.2 27.1 - - + -
135D LEU* 4.7 4.7 - - + -
138D VAL* 4.3 15.5 - - + -
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Residues in contact with TYR 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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110D ILE 2.9 18.2 + - - +
111D LYS 3.5 4.5 - - - +
113D LEU* 1.3 75.4 - - - +
115D VAL* 1.3 65.1 + - + +
118D GLY* 2.6 32.5 + - - +
119D ASP* 2.6 49.1 + - - +
120D LYS* 4.7 6.2 - - + +
122D LEU* 4.1 15.0 - - + -
124D ARG 3.6 1.2 + - - -
125D LEU* 3.6 15.0 - - + +
126D ARG 3.6 23.4 + - - -
127D ILE* 3.5 27.3 - - + +
165D ILE* 4.6 0.4 - - + -
173D PHE* 3.8 23.3 - + + -
178D LEU* 4.0 23.3 - - + -
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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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13D TYR* 3.7 11.2 - - + +
17D LEU* 3.8 14.8 - - + -
42D GLN* 4.6 6.3 - - - +
47D LEU* 4.3 25.4 - - + -
51D HIS* 6.0 0.7 - - + -
111D LYS 3.0 15.7 + - - +
112D GLY 3.3 7.6 + - - +
114D TYR* 1.3 78.8 - - + +
116D ALA* 1.3 63.6 + - - +
120D LYS* 3.4 23.8 + - + +
178D LEU* 6.0 0.7 - - + -
186D PRO* 3.4 35.7 - - + -
187D PRO* 5.8 1.6 - - + -
1190D MN 4.2 1.2 + - - -
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Residues in contact with ALA 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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16D GLY 4.2 3.8 - - - +
17D LEU* 4.2 7.6 - - + +
20D GLY* 3.8 22.0 - - - -
21D ASP* 3.3 31.6 - - + +
42D GLN* 5.2 1.1 - - - +
112D GLY 3.1 16.1 + - - +
113D LEU 3.8 2.9 - - - +
115D VAL* 1.3 78.7 - - - +
117D GLU* 1.3 61.2 + - - +
120D LYS* 4.1 0.2 + - - -
1190D MN 2.4 28.9 + - - -
16M C 3.0 7.8 + - - +
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Residues in contact with GLU 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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20D GLY* 3.5 18.6 - - - -
21D ASP* 3.0 2.9 - - - +
113D LEU* 2.8 27.5 + - + +
116D ALA* 1.3 74.3 - - - +
118D GLY* 1.3 62.3 + - - +
127D ILE* 4.1 8.7 - - + -
128D TRP* 3.1 49.7 + - - +
129D ASN* 3.1 8.7 + - - +
1189D MN 1.9 35.7 + - - -
1191D MN 2.2 32.0 + - - -
15F C 2.9 11.0 + - - +
16M C 3.3 7.5 + - - +
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Residues in contact with GLY 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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113D LEU 3.9 0.4 + - - -
114D TYR* 2.6 41.2 + - - -
115D VAL 4.6 0.2 - - - -
116D ALA 3.6 0.6 - - - -
117D GLU* 1.3 74.7 - - - +
119D ASP* 1.3 61.4 + - - -
120D LYS* 3.1 24.5 + - - -
126D ARG 3.0 10.8 - - - -
127D ILE* 4.4 1.3 - - - -
128D TRP* 3.9 2.5 - - - -
16M C 3.8 7.1 - - - +
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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