Contacts of the helix formed by residues 120 - 139 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASN 3.9 1.6 + - - -
113B PRO* 3.2 15.4 - - + +
114B HIS* 3.4 31.6 + - + +
118B THR* 3.2 6.1 + - - +
119B PHE* 1.3 71.5 - - - +
121B ILE* 1.3 56.8 + - - +
122B ASN* 4.0 7.8 + - - +
123B PHE* 3.2 28.5 + - + +
124B GLY 2.8 22.7 + - - -
26D TYR* 5.1 4.7 - - - -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 4.5 14.4 - - + -
222A ILE* 3.9 22.4 - - + -
16B LYS* 5.7 3.4 - - - -
18B LEU* 3.3 34.1 - - + -
110B ILE* 3.3 44.0 - - + +
111B ASN* 3.6 18.8 - - - +
119B PHE* 2.9 13.0 + - + +
120B ASP* 1.3 68.9 + - - +
122B ASN* 1.3 63.8 + - - +
125B LEU* 2.9 45.4 + - + +
151B THR* 6.0 0.2 - - + -
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Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 6.2 2.4 - - - +
17B GLU 4.4 10.7 + - - -
18B LEU* 3.5 14.4 - - - +
19B LEU* 2.9 47.4 + - + +
24B HIS* 3.5 10.7 + - - -
120B ASP* 3.4 6.0 + - - +
121B ILE* 1.3 80.6 - - - +
123B PHE* 1.3 61.4 + - - +
125B LEU* 4.9 3.0 - - - +
126B ARG* 3.1 23.7 + - - +
26D TYR* 4.0 24.2 + - + -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PRO* 3.7 13.9 - - + -
114B HIS* 3.6 28.3 - + - -
120B ASP* 3.2 32.0 + - - +
122B ASN* 1.3 76.7 - - - +
124B GLY* 1.3 53.8 + - - +
126B ARG* 3.2 5.2 + - + +
127B GLN* 2.7 70.5 + - + +
26D TYR* 3.4 22.7 + + + +
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.5 14.5 - - - +
110B ILE* 3.2 31.0 - - - -
113B PRO* 3.7 6.7 - - - -
120B ASP 2.8 11.8 + - - -
121B ILE 3.2 0.6 + - - -
123B PHE* 1.3 74.1 - - - +
125B LEU* 1.3 56.7 + - - +
127B GLN* 3.4 3.7 + - - +
128B ALA* 3.0 29.1 + - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 5.0 3.6 - - + -
18B LEU* 4.4 10.5 - - + -
24B HIS* 4.0 17.1 + - + +
110B ILE* 3.6 23.3 - - + -
121B ILE* 2.9 34.1 + - + +
122B ASN* 5.2 2.2 - - - +
124B GLY* 1.3 73.3 - - - +
126B ARG* 1.3 63.8 + - - +
128B ALA* 3.4 3.1 + - - +
129B ARG* 3.1 24.9 + - - +
151B THR* 4.5 7.6 - - + -
154B TYR* 3.9 54.1 - - + +
155B TYR* 4.1 18.3 - - + -
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.2 10.3 - - - +
23B ALA* 4.0 10.5 + - - +
24B HIS* 3.0 35.6 + - - +
27B GLU* 3.8 19.8 - - - +
28B LEU* 3.5 28.9 - - - +
122B ASN 3.1 19.6 + - - +
123B PHE* 3.5 7.0 - - + +
125B LEU* 1.3 77.2 - - - +
127B GLN* 1.3 58.3 + - - +
129B ARG* 3.4 2.8 + - - +
130B SER* 2.9 29.2 + - - -
26D TYR* 3.6 25.7 - - + +
27D GLU* 2.6 34.3 + - - -
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO* 3.5 34.6 - - + +
109B LEU* 3.6 20.1 - - + +
113B PRO* 3.6 23.8 + - - +
123B PHE* 2.7 45.1 + - + +
124B GLY 3.7 4.3 - - - +
126B ARG* 1.3 73.3 - - - +
128B ALA* 1.3 58.0 + - - +
130B SER* 3.3 6.7 + - - -
131B LEU* 3.0 30.2 + - - +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.4 37.1 - - + -
109B LEU* 4.9 1.3 - - + +
110B ILE* 3.9 17.7 - - + -
124B GLY 3.0 16.8 + - - +
125B LEU* 3.9 4.0 - - - +
127B GLN* 1.3 75.0 - - - +
129B ARG* 1.3 64.5 + - - +
131B LEU* 3.9 1.9 - - - +
132B LEU* 3.1 32.1 + - - +
155B TYR* 4.6 6.3 - - + -
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B HIS* 3.8 30.3 + - + -
25B LEU* 3.2 19.4 - - - +
28B LEU* 2.9 39.2 + - + -
30B ILE* 3.8 13.1 - - - +
125B LEU 3.1 17.0 + - - +
126B ARG* 3.8 4.5 - - - +
128B ALA* 1.3 77.0 - - - +
130B SER* 1.3 56.6 + - - +
132B LEU* 3.2 5.9 + - - +
133B LEU* 2.9 29.5 + - + +
154B TYR* 2.8 37.0 + - + +
155B TYR* 3.6 11.9 - - + +
157B ASP* 2.8 39.4 + - - -
158B LEU* 3.7 15.1 - - + +
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.8 21.6 - - - +
126B ARG* 2.9 19.8 + - - -
127B GLN* 3.3 8.7 + - - -
129B ARG* 1.3 78.4 - - - +
131B LEU* 1.3 57.6 + - - +
133B LEU* 3.3 6.1 + - - +
134B SER* 2.9 37.5 + - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.0 27.1 - - + -
68B PRO* 4.2 23.6 - - + +
71B ALA* 4.2 12.3 - - + -
72B LEU* 3.8 33.2 - - + -
95B VAL* 4.1 19.3 - - + -
97B PHE* 4.5 7.0 - - + -
109B LEU* 5.2 1.8 - - + -
127B GLN 3.0 15.8 + - - +
128B ALA* 3.9 4.7 - - - +
130B SER* 1.3 75.8 - - - +
132B LEU* 1.3 58.9 + - - +
134B SER* 3.3 4.7 + - - -
135B LEU* 2.9 46.3 + - + +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 3.7 24.2 - - + -
97B PHE* 4.2 12.3 - - + -
128B ALA 3.1 23.6 + - - +
129B ARG 3.7 3.8 - - - +
130B SER 3.2 0.2 - - - -
131B LEU* 1.3 78.8 - - - +
133B LEU* 1.3 62.2 + - - +
135B LEU* 3.4 4.3 + - + +
136B ASN* 2.8 32.0 + - - -
142B ALA* 3.6 28.9 - - + -
155B TYR* 3.6 42.6 - - + +
158B LEU* 3.7 14.1 - - + +
159B ILE* 3.9 17.3 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 4.0 31.6 - - + +
29B PRO 4.0 23.6 - - - +
30B ILE* 4.4 4.7 - - - -
31B SER* 4.3 12.6 - - - +
34B ALA* 4.3 9.0 - - + -
129B ARG* 2.9 18.3 + - + +
130B SER* 3.7 5.2 - - - +
132B LEU* 1.3 74.3 - - - +
134B SER* 1.3 60.5 - - - +
135B LEU 3.3 0.3 + - - -
136B ASN* 3.4 2.2 + - - +
137B ASN* 2.8 61.6 + - - +
158B LEU* 4.1 15.2 - - + +
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.9 23.5 - - - +
130B SER* 2.9 22.4 + - - -
131B LEU* 3.3 5.3 + - - -
133B LEU* 1.3 79.5 - - - +
135B LEU* 1.3 61.3 + - - +
137B ASN* 3.6 9.0 - - - +
138B MET* 3.1 26.3 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ALA 4.5 2.9 - - - +
72B LEU* 4.3 10.8 - - + -
75B ALA* 3.3 34.1 - - + -
93B MET* 3.8 13.5 - - + -
95B VAL* 3.8 31.9 - - + -
131B LEU* 2.9 42.0 + - + +
132B LEU* 3.7 7.4 - - - +
134B SER* 1.3 75.3 - - - +
136B ASN* 1.3 59.7 + - - +
138B MET* 3.0 16.2 - - - +
140B MET* 2.9 38.8 + - + +
142B ALA* 4.4 5.6 - - + -
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Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLU* 4.9 2.1 - - - +
34B ALA* 3.7 29.2 + - + -
37B LEU* 3.5 28.5 - - + +
38B VAL* 3.4 24.6 + - - +
132B LEU 2.8 26.0 + - - +
133B LEU* 3.9 1.6 - - - +
135B LEU* 1.3 79.6 - - - +
137B ASN* 1.3 57.7 + - - +
139B GLY* 3.0 15.9 + - - -
140B MET 3.6 7.7 + - - -
141B PRO* 4.0 9.1 - - - +
142B ALA* 4.6 6.3 + - - +
158B LEU* 3.2 29.5 + - - +
160B SER* 4.6 0.7 + - - -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER* 2.8 27.7 + - - -
33B GLU* 3.8 20.2 - - - +
34B ALA* 4.0 7.8 + - - +
133B LEU* 2.8 45.7 + - - +
134B SER* 3.6 8.1 - - - +
136B ASN* 1.3 74.0 - - - +
138B MET* 1.3 59.7 + - - +
139B GLY* 3.6 0.5 + - - -
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Residues in contact with MET 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.7 38.6 - - + +
75B ALA* 3.9 25.4 - - - -
76B GLU* 4.4 12.6 - - + -
79B LEU* 3.4 29.5 - - + +
134B SER* 3.1 13.2 + - - +
135B LEU* 3.0 19.5 - - - +
137B ASN* 1.3 75.2 - - - +
139B GLY* 1.3 56.0 + - - +
140B MET* 4.0 7.2 - - + +
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.6 16.1 - - - +
79B LEU* 3.4 12.3 - - - +
82B ARG* 3.4 14.7 + - - -
136B ASN 3.0 13.9 + - - -
137B ASN 3.3 1.2 + - - -
138B MET* 1.3 79.6 - - - +
140B MET* 1.3 59.7 + - - +
141B PRO* 3.3 10.4 - - - +
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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