Contacts of the helix formed by residues 120 - 139 (chain A) in PDB entry 4UC5
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 ASP 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASN 3.6 1.8 + - - -
113A PRO* 3.1 14.9 - - + +
114A HIS* 3.4 31.4 + - + +
118A THR* 3.2 5.1 + - - +
119A PHE* 1.3 70.9 - - - +
121A ILE* 1.3 58.2 + - - +
122A ASN* 3.8 7.3 + - - +
123A PHE* 3.2 30.7 + - + +
124A GLY 2.9 22.7 + - - -
26C TYR* 4.7 4.1 + - - -
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Residues in contact with ILE 121 (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 LYS* 5.7 4.3 - - - -
18A LEU* 3.2 32.5 - - + -
110A ILE* 3.4 40.4 - - + +
111A ASN* 3.7 18.6 - - - +
119A PHE 3.0 11.6 + - - +
120A ASP* 1.3 69.3 + - - +
122A ASN* 1.3 69.1 + - - +
125A LEU* 2.9 40.6 + - + +
212B LEU* 4.3 17.3 - - + -
222B ILE* 4.0 26.5 - - + -
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Residues in contact with ASN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 6.3 0.8 - - - +
17A GLU 4.9 3.4 + - - -
18A LEU* 3.8 16.6 - - - +
19A LEU* 3.0 48.9 + - + +
24A HIS* 3.6 12.5 + - - -
120A ASP* 3.4 6.1 + - - +
121A ILE* 1.3 80.1 - - - +
123A PHE* 1.3 62.2 + - - +
125A LEU* 4.9 2.4 - - - +
126A ARG* 3.3 20.3 + - - +
26C TYR* 3.8 27.5 + - + +
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Residues in contact with PHE 123 (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 PRO* 3.7 13.9 - - + -
114A HIS* 3.6 29.8 - + - -
120A ASP* 3.2 30.3 + - - +
121A ILE 3.2 0.6 - - - -
122A ASN* 1.3 77.9 - - - +
124A GLY* 1.3 58.5 + - - +
126A ARG* 3.2 8.8 + - + +
127A GLN* 2.9 61.2 + - + +
26C TYR* 3.6 13.9 + - - +
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Residues in contact with GLY 124 (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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109A LEU* 3.6 14.7 - - - +
110A ILE* 3.5 25.5 - - - -
113A PRO* 3.7 7.9 - - - -
120A ASP 2.9 10.5 + - - -
121A ILE 3.1 0.8 + - - -
123A PHE* 1.3 75.8 - - - +
125A LEU* 1.3 58.2 + - - +
127A GLN* 3.4 3.8 + - - +
128A ALA* 2.8 30.5 + - - +
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Residues in contact with LEU 125 (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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18A LEU* 4.4 10.3 - - + -
19A LEU 5.3 0.4 - - - +
24A HIS* 4.0 16.7 + - + +
110A ILE* 3.5 24.4 + - + -
121A ILE* 2.9 33.3 + - + +
122A ASN* 4.9 3.4 - - - +
124A GLY* 1.3 76.1 - - - +
126A ARG* 1.3 62.7 + - - +
128A ALA* 3.7 4.7 - - - +
129A ARG* 3.0 23.9 + - - +
151A THR* 4.4 9.6 - - + -
154A TYR* 3.8 54.0 - - + +
155A TYR* 4.4 15.0 - - + -
212B LEU* 5.5 1.8 - - + -
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Residues in contact with ARG 126 (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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19A LEU* 4.1 16.2 - - - +
23A ALA* 3.9 16.2 + - - +
24A HIS* 3.0 35.1 + - - +
27A GLU* 3.7 14.8 - - - +
28A LEU* 3.4 29.8 - - + +
122A ASN 3.3 12.0 + - - +
123A PHE* 3.2 14.3 + - + +
124A GLY 3.2 0.6 - - - -
125A LEU* 1.3 80.5 - - - +
127A GLN* 1.3 58.1 + - - +
129A ARG* 3.3 1.7 + - - -
130A SER* 2.9 30.6 + - - -
26C TYR* 4.2 11.7 - - + +
27C GLU* 2.8 34.2 + - - -
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Residues in contact with GLN 127 (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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68A PRO* 3.2 35.4 - - + +
109A LEU* 3.7 26.8 - - + +
113A PRO* 3.8 15.7 + - - +
123A PHE* 2.9 41.1 + - + +
124A GLY* 3.8 3.8 - - - +
126A ARG* 1.3 76.8 - - - +
128A ALA* 1.3 65.1 + - - +
130A SER* 3.7 6.3 - - - -
131A LEU* 3.1 24.8 + - - +
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Residues in contact with ALA 128 (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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97A PHE* 3.7 32.4 - - + -
109A LEU* 5.0 3.3 - - + +
110A ILE* 3.7 21.1 - - + -
124A GLY 2.8 18.3 + - - +
125A LEU* 3.7 5.2 - - - +
127A GLN* 1.3 78.6 - - - +
129A ARG* 1.3 62.8 + - - +
131A LEU* 3.5 2.1 + - - +
132A LEU* 3.1 29.2 + - - +
155A TYR* 4.6 6.1 - - + -
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Residues in contact with ARG 129 (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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24A HIS* 4.1 22.9 + - + -
25A LEU* 3.4 21.2 - - - +
28A LEU* 2.8 44.4 + - + +
30A ILE* 3.7 12.3 - - - +
125A LEU 3.0 17.3 + - - +
126A ARG* 3.9 4.5 - - - +
128A ALA* 1.3 77.1 - - - +
130A SER* 1.3 53.4 + - - +
132A LEU* 3.2 3.2 + - - +
133A LEU* 2.8 33.7 + - + +
154A TYR* 2.9 26.8 + - + +
155A TYR* 3.7 11.8 - - + +
157A ASP* 2.8 43.6 + - - -
158A LEU* 3.6 19.3 - - + +
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Residues in contact with SER 130 (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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28A LEU* 3.6 25.0 - - - +
126A ARG* 2.9 19.7 + - - -
127A GLN* 3.7 9.4 - - - -
129A ARG* 1.3 76.4 - - - +
131A LEU* 1.3 57.2 + - - +
133A LEU* 3.3 3.4 + - - +
134A SER* 2.8 38.4 + - - -
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Residues in contact with LEU 131 (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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65A ILE* 3.7 29.2 - - + -
68A PRO* 4.0 26.2 - - + +
71A ALA* 4.2 10.3 - - + -
72A LEU* 3.8 30.3 - - + -
95A VAL* 4.3 16.4 - - + -
97A PHE* 4.3 8.3 - - + -
109A LEU* 5.0 2.0 - - + -
127A GLN 3.1 15.5 + - - +
128A ALA 3.8 4.3 - - - +
130A SER* 1.3 77.7 - - - +
132A LEU* 1.3 63.3 + - - +
134A SER* 3.2 4.5 + - - -
135A LEU* 2.9 42.6 + - + +
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Residues in contact with LEU 132 (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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95A VAL* 3.8 22.9 - - + -
97A PHE* 4.1 13.9 - - + -
128A ALA 3.1 18.2 + - - +
129A ARG 3.6 3.4 - - - +
131A LEU* 1.3 78.8 - - - +
133A LEU* 1.3 63.2 + - - +
135A LEU* 3.3 4.6 + - + +
136A ASN* 3.0 31.7 + - - +
142A ALA* 3.5 30.3 - - + -
155A TYR* 3.7 40.4 - - + +
158A LEU* 4.0 14.8 - - + +
159A ILE* 3.8 17.7 - - + -
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Residues in contact with LEU 133 (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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28A LEU* 4.0 31.4 - - + +
29A PRO* 3.6 26.0 - - + +
30A ILE* 4.2 5.2 - - - -
31A SER* 4.1 14.6 - - - +
34A ALA* 4.2 12.8 - - + -
129A ARG 2.8 17.8 + - - +
130A SER* 3.7 4.9 - - - +
132A LEU* 1.3 77.4 - - - +
134A SER* 1.3 59.0 + - - +
136A ASN* 3.8 0.9 - - - +
137A ASN* 2.9 46.5 + - - +
158A LEU* 4.0 15.9 - - + +
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Residues in contact with SER 134 (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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72A LEU* 3.9 26.0 - - - +
130A SER* 2.8 24.2 + - - -
131A LEU* 3.6 5.8 - - - -
133A LEU* 1.3 76.9 - - - +
135A LEU* 1.3 59.9 + - - +
137A ASN* 3.4 10.2 + - - +
138A MET* 3.1 25.8 + - - +
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Residues in contact with LEU 135 (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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71A ALA 4.5 2.9 - - - +
72A LEU* 3.7 17.3 - - + -
75A ALA* 3.4 32.3 - - + -
93A MET* 4.2 12.8 - - + -
95A VAL* 3.7 31.0 - - + -
131A LEU* 2.9 39.8 + - + +
132A LEU* 3.8 7.6 - - - +
134A SER* 1.3 72.1 - - - +
136A ASN* 1.3 66.5 + - - +
138A MET* 3.2 8.6 + - + +
139A GLY 3.2 4.5 + - - -
140A MET* 2.9 37.8 + - + +
142A ALA* 4.5 5.4 - - + -
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Residues in contact with ASN 136 (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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33A GLU* 5.1 1.9 - - - +
34A ALA* 3.8 24.3 + - + -
37A LEU* 3.6 24.3 - - - +
38A VAL* 3.5 21.9 - - - +
132A LEU 3.0 23.8 + - - +
133A LEU* 3.8 4.0 - - - +
135A LEU* 1.3 80.5 - - - +
137A ASN* 1.3 56.3 + - - +
139A GLY* 2.9 20.8 + - - -
140A MET 3.8 6.3 - - - -
141A PRO* 3.9 9.0 - - - +
142A ALA* 4.5 6.9 - - - +
158A LEU* 3.0 34.6 + - - +
160A SER* 4.7 0.5 + - - -
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Residues in contact with ASN 137 (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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31A SER* 2.7 29.9 + - - -
33A GLU* 3.5 20.3 - - - +
34A ALA* 3.9 5.1 + - - +
133A LEU* 2.9 40.6 + - - +
134A SER* 3.6 8.5 - - - +
135A LEU 3.3 0.2 - - - -
136A ASN* 1.3 77.0 - - - +
138A MET* 1.3 58.2 + - - +
139A GLY 3.2 0.8 + - - -
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Residues in contact with MET 138 (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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72A LEU* 3.6 43.1 - - + +
75A ALA* 3.8 26.0 - - + +
76A GLU* 4.1 15.7 - - + -
79A LEU* 3.4 25.5 - - + +
134A SER* 3.1 13.1 + - - +
135A LEU* 3.2 15.7 + - + +
136A ASN 3.2 0.4 - - - -
137A ASN* 1.3 75.3 - - - +
139A GLY* 1.3 55.3 + - - +
140A MET* 4.0 7.0 - - + +
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Residues in contact with GLY 139 (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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37A LEU* 3.7 13.8 - - - +
79A LEU* 3.5 13.0 - - - +
82A ARG* 3.5 13.5 + - - -
136A ASN 2.9 12.6 + - - -
137A ASN 3.2 1.0 + - - -
138A MET* 1.3 78.4 - - - +
140A MET* 1.3 58.8 + - - +
141A PRO* 3.2 12.0 - - - +
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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
------------------------------------------------------------
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