Contacts of the helix formed by residues 102 - 118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 5.2 3.7 + - - -
100A LEU 3.3 3.5 + - - +
101A PHE* 1.3 74.9 - - - +
103A MET* 1.3 59.7 + - - +
104A ARG* 3.3 11.0 + - - +
105A GLU* 3.0 42.8 + - - +
106A GLN* 2.8 29.3 + - - +
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Residues in contact with MET 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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102A ASN* 1.3 75.5 - - - +
104A ARG* 1.3 62.0 + - - +
106A GLN* 3.9 16.8 - - - +
107A ILE* 3.2 41.5 + - + +
144A ASN 5.6 3.8 - - - +
145A LEU* 4.2 23.8 - - + -
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Residues in contact with ARG 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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5A GLU* 3.1 57.9 + - - +
6A ASN* 4.9 3.2 - - - +
8A SER* 4.3 4.5 - - - +
9A GLY* 4.6 9.0 - - - -
102A ASN* 3.1 13.4 + - - +
103A MET* 1.3 80.4 - - - +
105A GLU* 1.3 61.3 + - + +
107A ILE* 4.1 3.1 - - - +
108A ALA* 3.3 22.3 + - - +
182A LEU* 4.5 23.1 - - + +
183A ASN* 3.5 42.0 - - - +
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Residues in contact with GLU 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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8A SER* 3.7 40.1 - - - +
9A GLY* 5.2 0.4 - - - -
12A ALA* 3.4 11.7 - - + +
94A MET* 4.0 11.3 - - - +
97A ARG* 4.2 15.1 + - - -
100A LEU 4.5 0.9 - - - +
101A PHE* 3.3 33.5 - - + -
102A ASN* 3.0 41.5 + - - +
104A ARG* 1.3 76.2 - - - +
106A GLN* 1.3 60.4 + - - +
108A ALA* 3.3 0.6 + - - -
109A PHE* 2.8 32.7 + - - +
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Residues in contact with GLN 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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99A ARG 5.4 0.4 + - - -
101A PHE* 2.7 27.8 + - + +
102A ASN* 2.8 22.9 + - - +
103A MET* 3.9 13.7 - - - +
104A ARG 3.4 0.2 - - - -
105A GLU* 1.3 77.5 - - - +
107A ILE* 1.3 65.0 + - + +
109A PHE* 3.6 1.4 - - - +
110A ILE* 2.9 32.5 + - + +
141A TRP* 3.4 66.2 - - + +
144A ASN* 5.8 1.9 - - - +
145A LEU* 4.6 9.8 - - + +
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Residues in contact with ILE 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 MET* 3.2 35.1 + - + +
104A ARG* 4.1 3.4 - - - +
106A GLN* 1.3 77.1 - - + +
108A ALA* 1.3 58.1 + - - +
110A ILE* 3.4 2.2 + - - +
111A LYS* 2.9 27.9 + - - +
145A LEU* 4.3 14.8 - - + -
176A THR* 3.3 39.0 - - + +
177A ILE* 3.7 28.0 - - + +
180A SER* 4.1 14.8 - - - +
182A LEU* 4.6 20.0 - - + -
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Residues in contact with ALA 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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9A GLY* 3.3 31.0 - - - +
12A ALA* 3.8 5.6 - - + -
13A TYR* 3.4 20.0 - - + +
104A ARG 3.3 16.6 + - - +
106A GLN 3.3 0.6 - - - -
107A ILE* 1.3 78.7 - - - +
109A PHE* 1.3 58.5 + - - +
111A LYS* 3.4 8.6 + - - +
112A GLY 2.9 24.3 + - - -
183A ASN* 4.3 9.4 - - - +
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Residues in contact with PHE 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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12A ALA 3.5 20.7 + - - +
15A LEU* 3.9 13.9 - - + -
16A GLY* 3.8 9.6 - - - -
19A ILE* 3.6 34.5 - - + -
98A ILE* 3.6 25.1 - - + -
101A PHE* 4.1 13.7 - + + -
105A GLU 2.8 22.1 + - - +
106A GLN 3.6 3.4 - - - +
108A ALA* 1.3 73.4 - - - +
110A ILE* 1.3 59.9 + - - +
112A GLY* 3.2 1.4 + - - -
113A LEU* 2.8 45.9 + - + +
134A LEU* 3.7 27.8 - - + -
138A VAL* 4.3 6.7 - - + -
141A TRP* 3.9 17.0 - + + -
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Residues in contact with ILE 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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106A GLN* 2.9 27.5 + - + +
107A ILE 3.9 0.9 - - - +
109A PHE* 1.3 76.6 - - - +
111A LYS* 1.3 56.9 + - - +
113A LEU* 3.7 6.0 - - - +
114A TYR* 2.8 28.8 + - - +
127A ILE* 4.7 8.4 - - + +
138A VAL* 4.1 25.8 - - + -
141A TRP* 4.2 27.8 - - + -
142A LEU* 4.2 21.3 - - + -
145A LEU* 4.7 3.8 - - + -
173A PHE* 4.1 17.3 - - + -
177A ILE* 3.6 29.8 - - + -
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Residues in contact with LYS 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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13A TYR* 3.7 22.4 - - + -
107A ILE 2.9 18.1 + - - +
108A ALA* 3.5 7.0 - - - +
110A ILE* 1.3 77.6 - - - +
112A GLY* 1.3 57.1 + - - +
114A TYR* 3.3 4.8 + - - +
115A VAL* 2.9 39.9 + - + +
177A ILE* 3.3 27.2 - - - +
178A LEU* 2.8 26.6 + - + +
179A SER* 4.3 1.6 - - - +
180A SER* 2.9 35.1 + - - +
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Residues in contact with GLY 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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13A TYR* 3.5 36.1 - - - -
16A GLY 3.7 6.7 - - - -
17A LEU* 3.3 13.5 - - - +
108A ALA 2.9 11.7 + - - -
109A PHE 3.7 1.8 - - - -
111A LYS* 1.3 75.8 - - - +
113A LEU* 1.3 63.2 + - - +
115A VAL 3.2 1.6 + - - -
116A ALA* 3.0 19.8 + - - +
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Residues in contact with LEU 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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16A GLY* 3.6 20.5 - - - +
19A ILE* 4.1 13.7 - - + -
20A GLY* 4.1 17.9 - - - +
109A PHE* 2.8 40.6 + - + +
110A ILE* 3.7 6.5 - - - +
112A GLY* 1.3 71.5 - - - -
114A TYR* 1.3 52.7 + - - +
116A ALA* 3.2 2.1 + - - +
117A GLU* 2.6 41.2 + - + +
127A ILE* 4.1 27.8 - - + -
129A ASN* 5.3 2.7 - - - +
134A LEU* 4.4 13.5 - - + -
135A LEU* 4.7 5.2 - - + -
138A VAL* 4.2 17.3 - - + -
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ILE 2.8 19.1 + - - +
111A LYS 3.7 0.9 - - - +
113A LEU* 1.3 73.6 - - - +
115A VAL* 1.3 68.4 + - + +
116A ALA 3.1 1.3 - - - -
118A GLY* 2.8 28.4 + - - +
119A ASP 2.6 39.2 + - - -
120A LYS* 3.4 8.8 - - + -
122A LEU* 4.2 2.5 - - + -
125A LEU* 3.4 19.6 - - + +
126A ARG 3.4 28.5 + - - -
127A ILE* 3.6 22.9 - - + +
165A ILE* 4.4 1.8 - - + -
173A PHE* 3.7 26.9 - + + -
178A LEU* 3.7 35.2 - - + -
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Residues in contact with VAL 115 (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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13A TYR* 3.8 22.4 - - + +
17A LEU* 3.9 15.9 - - + -
42A GLN* 4.6 6.9 - - - +
47A LEU* 4.3 26.0 - - + -
111A LYS* 2.9 29.7 + - + +
112A GLY 3.6 6.5 - - - +
114A TYR* 1.3 76.4 - - + +
116A ALA* 1.3 58.1 + - - +
120A LYS* 3.0 28.0 + - + +
178A LEU* 6.0 1.8 - - + -
1188A MN 4.2 2.1 + - - -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY 4.3 2.0 - - - +
17A LEU* 4.0 9.4 - - + +
20A GLY* 3.9 10.8 - - - -
21A ASP* 3.2 42.0 - - + +
42A GLN* 5.2 0.4 - - - +
112A GLY 3.0 14.6 + - - +
113A LEU 3.6 6.3 - - - +
115A VAL* 1.3 78.0 - - - +
117A GLU* 1.3 59.9 + - - +
118A GLY 3.6 0.4 - - - -
120A LYS* 3.1 5.5 + - - -
1188A MN 2.3 27.0 + - - -
16K C 2.8 5.2 - - - -
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Residues in contact with GLU 117 (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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20A GLY* 3.2 18.7 - - - +
21A ASP* 3.5 0.3 - - - +
113A LEU* 2.6 27.3 + - + +
116A ALA* 1.3 74.8 - - - +
118A GLY* 1.3 58.7 + - - +
127A ILE* 4.0 8.5 - - + -
128A TRP* 3.2 48.2 + - - +
129A ASN* 2.8 19.1 + - - +
1189A MN 2.2 31.7 + - - -
1190A MN 2.4 31.2 + - - -
15B G 3.1 0.2 + - - -
15C C 2.8 8.8 + - - +
16K C 3.6 8.3 - - - +
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Residues in contact with GLY 118 (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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113A LEU 3.9 0.4 + - - -
114A TYR* 2.8 34.9 + - - -
116A ALA 3.6 1.0 - - - -
117A GLU* 1.3 80.4 - - - +
119A ASP* 1.3 63.4 + - - -
120A LYS* 3.0 23.8 + - - -
126A ARG 3.1 10.1 - - - -
127A ILE* 4.4 0.9 - - - -
128A TRP* 3.9 2.2 - - - -
16K C 3.6 7.8 - - - +
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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