Contacts of the helix formed by residues 118 - 130 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASN 3.1 17.3 - - - -
37B ASN* 3.1 19.3 - - - +
39B ASP* 5.1 0.4 + - - -
117B GLY* 1.3 71.4 - - - +
119B GLN* 1.3 65.6 + - - -
121B GLY 3.2 1.0 + - - -
122B ILE* 3.0 29.6 + - - +
1001B SO4 3.5 15.9 + - - -
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Residues in contact with GLN 119 (chain B).
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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35B ASN* 2.9 13.5 + - - +
118B GLY* 1.3 71.2 - - - -
120B ALA* 1.3 59.2 + - - +
122B ILE* 3.5 2.9 + - - +
123B ILE* 2.9 40.0 + - + +
243B SER* 3.4 23.5 - - - +
244B GLY 3.6 0.7 + - - -
246B GLN* 2.8 29.8 + - - +
282B GLU* 3.4 14.0 + - - +
283B PHE 3.3 24.5 + - - -
284B ALA* 4.4 2.9 - - - +
455B ASP* 3.1 41.3 + - - +
1001B SO4 3.1 13.4 + - - +
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Residues in contact with ALA 120 (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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32B THR* 3.4 18.4 + - - +
33B ALA* 3.5 42.6 - - - +
34B TYR 4.3 0.7 - - - -
35B ASN* 3.0 20.2 + - - +
36B ALA* 5.5 0.9 - - + -
119B GLN* 1.3 79.4 - - - +
121B GLY* 1.3 56.8 + - - +
123B ILE* 3.4 4.3 + - - +
124B ALA* 2.9 25.3 + - - +
137B ALA* 5.7 1.8 - - + -
138B TYR 4.8 2.0 - - - +
150B PHE* 5.5 0.2 - - - -
241B ILE* 5.3 0.7 - - - +
243B SER* 3.7 2.9 + - - +
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Residues in contact with GLY 121 (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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35B ASN 3.2 7.3 + - - -
36B ALA* 4.2 9.5 - - - +
116B LEU* 3.1 30.9 - - - +
118B GLY 3.2 6.5 + - - -
120B ALA* 1.3 73.9 - - - +
122B ILE* 1.3 58.9 + - - +
124B ALA* 3.2 3.5 + - - +
125B ASN 2.9 24.3 + - - -
150B PHE* 4.0 13.5 - - - -
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Residues in contact with ILE 122 (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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39B ASP* 5.5 1.1 - - - +
116B LEU* 4.1 18.8 - - + +
117B GLY* 4.0 15.0 - - - -
118B GLY 3.0 24.5 + - - +
119B GLN* 3.9 4.9 - - - +
121B GLY* 1.3 72.9 - - - +
123B ILE* 1.3 64.8 + - + +
125B ASN* 3.4 4.8 + - - +
126B THR* 3.0 29.0 + - - +
391B ARG* 3.7 37.0 - - - +
451B VAL* 4.8 13.0 - - + +
452B GLY* 4.4 20.0 - - - +
455B ASP* 4.5 12.3 - - + +
456B THR* 4.5 4.9 - - - +
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Residues in contact with ILE 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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32B THR* 3.8 8.7 - - + -
119B GLN* 2.9 32.2 + - + +
120B ALA* 3.9 6.3 - - - +
122B ILE* 1.3 77.7 - - + +
124B ALA* 1.3 62.8 + - - +
126B THR* 3.3 6.0 + - - -
127B LEU* 3.1 33.0 + - + +
241B ILE* 3.8 46.4 - - + -
243B SER* 5.2 1.6 - - - +
282B GLU* 4.9 7.9 - - + -
455B ASP* 3.8 40.2 - - + +
456B THR* 6.4 0.7 - - - +
458B SER* 5.8 1.8 - - - -
459B ALA* 4.0 12.1 - - + +
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Residues in contact with ALA 124 (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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32B THR* 3.7 15.7 + - - +
120B ALA 2.9 18.2 + - - +
121B GLY 3.2 5.4 + - - +
123B ILE* 1.3 77.5 - - - +
125B ASN* 1.3 63.0 + - - +
127B LEU* 3.4 0.4 + - - -
128B ALA* 3.0 24.8 + - - +
135B VAL* 3.6 22.6 - - + +
137B ALA* 3.9 16.4 - - + -
150B PHE* 4.4 2.9 - - + -
154B VAL* 4.1 9.2 - - + -
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Residues in contact with ASN 125 (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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116B LEU* 3.3 30.2 - - + +
121B GLY 2.9 11.6 + - - +
122B ILE* 4.0 5.8 - - - +
123B ILE 3.4 0.2 - - - -
124B ALA* 1.3 74.8 - - - +
126B THR* 1.3 57.8 + - - +
128B ALA* 3.3 2.3 + - - -
129B GLY 2.9 23.9 + - - -
149B LEU 3.5 15.0 + - - -
150B PHE* 3.6 9.5 - - - -
151B LYS* 2.9 56.2 + - - +
154B VAL* 3.9 1.7 - - - +
396B ASP* 5.6 0.7 - - - +
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Residues in contact with THR 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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122B ILE* 3.0 18.7 + - - +
123B ILE* 3.6 7.0 - - - -
124B ALA 3.2 0.2 - - - -
125B ASN* 1.3 78.0 - - - +
127B LEU* 1.3 65.8 + - + +
129B GLY* 3.2 3.5 + - - -
130B LEU* 3.1 22.8 + - + +
151B LYS* 5.4 0.2 - - - +
387B LEU* 4.1 27.8 - - + -
391B ARG* 3.8 21.8 + - - -
397B ILE* 4.2 23.3 + - + +
456B THR* 4.3 12.1 + - + -
459B ALA* 5.3 4.7 - - + -
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Residues in contact with LEU 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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30B ILE* 3.8 32.3 - - + -
32B THR* 4.4 3.4 - - + -
123B ILE* 3.1 36.5 + - + +
124B ALA* 4.1 2.2 - - - +
126B THR* 1.3 77.9 - - + +
128B ALA* 1.3 62.1 + - - +
130B LEU* 3.2 20.5 + - + +
131B LYS 3.3 8.3 + - - -
132B ILE* 3.6 25.9 + - + +
135B VAL* 3.7 16.8 - - + -
241B ILE* 4.3 3.6 - - + -
459B ALA* 4.5 20.2 - - + +
460B GLY* 6.0 0.2 - - - -
463B LEU* 4.4 24.0 - - + -
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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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124B ALA 3.0 18.3 + - - +
125B ASN 3.7 3.4 - - - +
127B LEU* 1.3 76.6 - - - +
129B GLY* 1.3 58.3 + - - +
131B LYS* 3.0 24.7 + - - +
135B VAL* 3.7 11.1 - - + +
151B LYS* 4.2 7.4 - - + -
152B LYS 4.2 17.4 - - - +
153B GLY* 4.6 2.7 - - - -
154B VAL* 3.7 25.6 - - + +
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Residues in contact with GLY 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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125B ASN 2.9 12.6 + - - -
126B THR 3.2 4.9 + - - -
128B ALA* 1.3 77.3 - - - +
130B LEU* 1.3 58.6 + - - +
131B LYS* 3.5 1.7 + - - +
151B LYS* 4.0 5.6 - - - +
397B ILE* 3.6 29.6 - - - -
398B ARG 4.0 6.7 - - - +
399B GLY* 3.0 30.5 - - - -
400B PRO* 3.1 2.9 - - - +
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Residues in contact with LEU 130 (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 ILE* 3.7 36.9 - - + +
26B GLU* 5.2 0.9 - - - +
126B THR 3.1 14.6 + - - +
127B LEU* 3.6 16.8 - - + +
128B ALA 3.1 0.6 - - - -
129B GLY* 1.3 76.9 - - - +
131B LYS* 1.3 70.2 + - - +
132B ILE* 3.4 7.4 + - + -
383B PHE* 4.5 9.2 - - + -
387B LEU* 4.1 32.1 - - + -
397B ILE* 4.0 17.0 - - + -
400B PRO* 3.9 19.7 - - + +
403B TYR* 4.8 4.7 - - + -
463B LEU* 4.5 21.1 - - + -
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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