Contacts of the helix formed by residues 128 - 138 (chain B) in PDB entry 3UCD
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 PRO 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLU 4.7 0.9 - - - +
127B LEU* 1.3 88.4 - - + +
129B LEU* 1.3 66.7 + - - +
130B TYR* 3.2 42.2 - - + +
131B ARG* 2.9 35.5 + - + +
132B HIS* 3.1 10.2 + - - +
415B GLU* 5.8 2.7 - - + -
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Residues in contact with LEU 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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118B CYS* 4.0 33.0 - - - +
119B LYS* 4.0 22.0 - - + -
122B ALA* 3.7 12.6 - - + +
127B LEU 3.5 1.2 + - - -
128B PRO* 1.3 73.4 - - - +
130B TYR* 1.3 63.8 + - - +
132B HIS* 3.1 3.0 + - + +
133B ILE* 2.9 36.3 + - + +
379B PHE* 3.8 29.2 - - + -
382B ASP* 3.3 32.8 + - + +
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Residues in contact with TYR 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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128B PRO* 3.5 25.0 - - + +
129B LEU* 1.3 75.5 - - - +
131B ARG* 1.4 89.7 + - + +
133B ILE* 3.6 0.8 + - - +
134B ALA* 2.9 22.9 + - - +
142B LEU* 3.7 22.4 - - + +
382B ASP* 3.1 49.4 + - - +
385B VAL* 4.1 19.7 - - + -
386B GLY* 3.3 12.4 - - - +
408B GLN* 5.9 0.2 - - - -
412B ILE* 3.8 31.2 - - + -
415B GLU* 3.3 30.8 - - + +
416B LEU* 4.0 14.0 - - + +
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Residues in contact with ARG 131 (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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127B LEU* 4.2 18.4 - - + -
128B PRO* 2.9 28.1 + - + +
130B TYR* 1.4 98.9 + - + +
132B HIS* 1.3 60.0 + - - +
134B ALA* 3.3 7.3 + - - +
135B GLN* 2.9 35.5 + - - +
140B SER 5.4 5.5 + - - -
142B LEU* 3.5 20.2 - - + +
416B LEU* 3.6 15.1 - - - +
419B GLU* 2.8 29.3 + - - -
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL 4.9 2.0 + - - -
84B VAL* 4.6 10.9 + - - -
86B GLN* 4.8 2.2 + - - -
118B CYS* 3.3 40.6 + - - -
121B GLY* 3.7 17.2 - - - -
122B ALA* 3.4 27.8 + - + -
125B ARG* 3.9 23.5 + - + +
127B LEU* 4.0 13.3 - - + +
128B PRO 3.1 6.6 + - - +
129B LEU* 3.5 7.2 - - + +
131B ARG* 1.3 75.5 - - - +
133B ILE* 1.3 56.5 + - - +
135B GLN* 3.1 7.2 + - + +
136B LEU* 2.9 57.4 + - + +
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Residues in contact with ILE 133 (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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118B CYS* 4.0 19.7 - - - -
129B LEU* 2.9 36.5 + - + +
130B TYR 3.8 4.0 - - - +
132B HIS* 1.3 74.3 - - - +
134B ALA* 1.3 65.0 + - - +
136B LEU* 3.1 10.2 + - + +
137B ALA* 3.0 21.5 + - - +
349B VAL* 5.7 0.4 - - + -
353B ILE* 4.6 6.9 - - + +
379B PHE* 3.8 19.1 - - + -
382B ASP 4.0 2.0 - - - -
383B LEU* 3.7 38.6 - - + +
386B GLY* 4.2 8.3 - - - -
387B LEU* 3.9 26.2 - - + -
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Residues in contact with ALA 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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130B TYR 2.9 16.1 + - - +
131B ARG* 3.4 10.1 - - - +
133B ILE* 1.3 76.7 - - - +
135B GLN* 1.3 56.4 + - + +
137B ALA* 3.2 1.8 + - - -
138B GLY 2.8 9.5 + - - -
139B ASN* 2.8 43.8 + - + +
140B SER 5.9 0.2 - - - -
142B LEU* 3.9 17.9 - - + -
386B GLY 3.2 21.1 + - - +
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Residues in contact with GLN 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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125B ARG* 4.9 10.4 + - - -
127B LEU* 3.3 36.0 - - - +
131B ARG* 2.9 16.4 + - - +
132B HIS* 3.5 10.3 + - - +
134B ALA* 1.3 76.8 - - + +
136B LEU* 1.3 64.2 + - + +
138B GLY* 3.3 11.5 + - - +
139B ASN 4.7 4.5 - - - +
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Residues in contact with LEU 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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84B VAL 4.5 7.0 - - - +
86B GLN* 4.0 36.6 - - + +
118B CYS* 4.1 15.9 - - - -
132B HIS* 2.9 46.6 + - + +
133B ILE* 3.5 9.6 - - - +
135B GLN* 1.3 78.6 - - - +
137B ALA* 1.3 59.3 - - - +
138B GLY 3.7 0.2 + - - -
353B ILE* 4.0 25.2 - - + +
357B LYS* 5.1 2.3 + - - +
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Residues in contact with ALA 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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133B ILE 3.0 10.5 + - - +
134B ALA 3.2 0.9 + - - +
136B LEU* 1.3 76.8 - - - +
138B GLY* 1.3 61.2 + - - +
139B ASN* 3.6 19.5 - - - +
353B ILE* 3.9 15.0 - - + -
357B LYS* 3.0 32.1 + - + +
387B LEU* 3.4 33.0 - - + -
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Residues in contact with GLY 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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134B ALA 2.8 4.1 + - - -
135B GLN* 3.3 12.2 + - - -
136B LEU 3.4 0.4 + - - -
137B ALA* 1.3 79.4 - - - +
139B ASN* 1.3 63.9 + - - +
140B SER* 4.2 0.7 + - - -
357B LYS* 4.7 3.4 - - - -
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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
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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