Contacts of the helix formed by residues 118 - 130 (chain A) in PDB entry 1U2X
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 GLY 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASN 3.3 16.6 - - - -
37A ASN* 3.2 18.4 - - - +
39A ASP* 4.9 0.2 + - - -
117A GLY* 1.3 72.5 - - - -
119A GLN* 1.4 66.6 + - - -
121A GLY 3.2 1.9 + - - -
122A ILE* 3.0 29.5 + - - +
1003A SO4 3.5 15.2 + - - -
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Residues in contact with GLN 119 (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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35A ASN* 3.0 12.0 + - - +
118A GLY* 1.4 70.6 - - - +
120A ALA* 1.3 58.5 + - - +
122A ILE* 3.4 3.0 + - - +
123A ILE* 2.9 39.5 + - + +
243A SER* 3.3 22.8 - - - +
244A GLY 3.6 1.0 + - - -
246A GLN* 2.8 29.2 + - - +
282A GLU* 3.5 11.6 + - + +
283A PHE 3.1 25.9 + - - -
284A ALA* 4.3 2.6 - - - +
455A ASP* 3.2 41.0 + - - +
1003A SO4 3.2 12.3 + - - +
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Residues in contact with ALA 120 (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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32A THR* 3.3 19.2 + - - +
33A ALA* 3.6 42.8 - - - +
34A TYR 4.3 0.4 - - - -
35A ASN* 3.0 20.8 + - - +
36A ALA* 5.4 1.3 - - + -
119A GLN* 1.3 76.7 - - - +
121A GLY* 1.3 56.5 + - - +
123A ILE* 3.8 3.7 - - - +
124A ALA* 2.9 25.8 + - - +
137A ALA* 5.6 1.6 - - + -
138A TYR 4.8 2.2 - - - +
150A PHE* 5.2 0.9 - - - -
241A ILE* 6.5 0.2 - - - -
243A SER* 3.6 2.4 + - - +
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Residues in contact with GLY 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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35A ASN 3.3 5.3 + - - -
36A ALA* 4.1 11.0 - - - +
116A LEU* 3.2 30.8 - - - +
118A GLY 3.2 6.7 + - - -
120A ALA* 1.3 74.1 - - - +
122A ILE* 1.3 58.4 + - - +
124A ALA* 3.2 2.6 + - - +
125A ASN* 2.9 24.9 + - - +
150A PHE* 3.8 13.7 - - - -
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Residues in contact with ILE 122 (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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39A ASP* 6.0 0.2 - - - +
116A LEU* 4.1 18.4 - - - +
117A GLY* 4.3 5.4 + - - -
118A GLY 3.0 30.0 + - - +
119A GLN* 3.8 4.0 - - - +
121A GLY* 1.3 70.2 - - - +
123A ILE* 1.3 67.4 + - + +
125A ASN* 3.4 4.8 + - - +
126A THR* 2.9 29.0 + - - +
391A ARG* 3.9 34.1 - - - +
451A VAL* 4.7 7.9 - - + +
452A GLY* 4.1 31.4 - - - +
455A ASP* 4.5 11.9 - - + +
456A THR* 4.2 6.5 - - - +
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Residues in contact with ILE 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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32A THR* 3.7 21.5 - - + -
119A GLN* 2.9 28.5 + - + +
120A ALA* 3.9 4.7 - - - +
122A ILE* 1.3 78.6 - - + +
124A ALA* 1.3 64.9 + - - +
126A THR* 3.2 5.1 + - - -
127A LEU* 3.0 28.5 + - + +
241A ILE* 3.7 39.9 - - + -
243A SER* 5.3 1.1 - - - +
282A GLU* 5.0 7.6 - - + -
455A ASP* 3.8 39.3 - - + +
456A THR* 5.5 0.4 - - - +
458A SER* 5.8 1.1 - - - -
459A ALA* 4.0 13.9 - - + +
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Residues in contact with ALA 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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32A THR* 3.8 14.8 + - - +
120A ALA 2.9 19.0 + - - +
121A GLY 3.5 4.3 - - - +
123A ILE* 1.3 80.2 - - - +
125A ASN* 1.3 63.1 + - - +
127A LEU* 4.7 0.2 - - - -
128A ALA* 3.0 25.8 + - - +
135A VAL* 3.7 20.2 - - + +
137A ALA* 3.9 17.9 - - + -
150A PHE* 4.2 8.3 - - + -
154A VAL* 4.3 5.8 - - + -
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Residues in contact with ASN 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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116A LEU* 3.4 28.5 - - + +
121A GLY 2.9 12.1 + - - +
122A ILE* 3.9 5.2 - - - +
123A ILE 3.2 0.2 - - - -
124A ALA* 1.3 78.9 - - - +
126A THR* 1.3 57.0 + - - +
128A ALA* 4.6 1.3 - - - -
129A GLY 2.9 23.9 + - - -
149A LEU 3.5 14.1 + - - -
150A PHE* 3.4 10.9 - - - -
151A LYS* 2.8 54.6 + - - +
154A VAL* 4.1 1.9 - - - +
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Residues in contact with THR 126 (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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122A ILE 2.9 18.3 + - - -
123A ILE* 3.7 6.1 - - - -
125A ASN* 1.3 74.6 - - - +
127A LEU* 1.3 62.9 + - + +
129A GLY* 3.1 3.6 + - - -
130A LEU* 3.0 22.8 + - + +
387A LEU* 3.9 29.2 - - + -
391A ARG* 3.8 20.6 + - - -
397A ILE* 4.2 23.5 + - + +
456A THR* 4.1 18.3 + - + -
459A ALA* 5.2 5.8 - - + -
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Residues in contact with LEU 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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30A ILE* 3.5 39.5 - - + -
32A THR* 4.5 4.7 - - + -
123A ILE* 3.0 34.1 + - + +
124A ALA 3.9 1.1 - - - +
126A THR* 1.3 76.3 - - + +
128A ALA* 1.4 60.9 + - - +
130A LEU* 3.2 23.6 + - + +
131A LYS 3.3 7.8 + - - -
132A ILE* 3.5 16.3 + - + +
135A VAL* 3.6 16.4 - - + -
241A ILE* 4.5 3.6 - - + -
459A ALA* 4.4 20.0 - - + +
463A LEU* 4.3 30.7 - - + -
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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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124A ALA 3.0 18.7 + - - +
125A ASN 3.9 3.4 - - - +
127A LEU* 1.4 72.4 - - - +
129A GLY* 1.3 65.6 + - - +
131A LYS* 3.1 21.8 + - - +
132A ILE 5.2 0.4 - - - +
135A VAL* 3.7 12.5 - - + +
151A LYS* 4.4 7.4 - - + -
152A LYS 4.4 15.6 - - - +
153A GLY* 4.7 3.1 - - - +
154A VAL* 3.7 24.5 - - + +
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Residues in contact with GLY 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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125A ASN 2.9 12.8 + - - -
126A THR 3.1 4.9 + - - -
128A ALA* 1.3 78.1 - - - +
130A LEU* 1.4 56.7 + - - +
131A LYS* 3.1 2.4 + - - +
151A LYS* 3.9 6.4 - - - +
397A ILE* 3.3 30.3 - - - -
398A ARG 3.6 5.4 - - - +
399A GLY* 3.0 32.7 - - - -
400A PRO* 3.6 0.7 - - - +
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Residues in contact with LEU 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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24A ILE* 3.8 34.4 - - + +
26A GLU* 5.4 1.0 - - - +
126A THR 3.0 17.1 + - - +
127A LEU* 3.2 18.8 + - + +
129A GLY* 1.4 73.3 - - - +
131A LYS* 1.3 69.3 + - - +
132A ILE* 3.4 8.5 + - + -
383A PHE* 4.5 7.6 - - + -
387A LEU* 4.0 41.1 - - + -
397A ILE* 4.0 12.3 - - + -
400A PRO* 3.6 21.9 - - + +
403A TYR* 4.4 8.7 - - + -
463A LEU* 4.3 22.2 - - + -
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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