Contacts of the helix formed by residues 114 - 125 (chain B) in PDB entry 1UHG
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 LEU 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B PRO 3.8 0.4 + - - -
113B ILE* 1.3 69.5 - - - +
115B PRO* 1.3 64.5 - - + +
116B GLU* 3.0 29.6 - - + +
117B TYR* 2.6 27.7 + - - +
118B LEU 3.0 8.7 + - - -
313B SER 3.3 26.2 - - - +
314B GLY* 3.4 18.8 - - - +
315B ILE 2.9 19.0 + - - +
316B SER 4.7 0.4 - - - -
317B SER* 3.9 31.6 - - - +
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Residues in contact with PRO 115 (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 ILE 3.1 8.1 - - - +
114B LEU* 1.3 84.6 - - + +
116B GLU* 1.3 76.9 + - - +
118B LEU* 3.6 9.7 - - + +
119B GLN* 2.8 33.3 + - - +
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 2.8 40.2 + - + +
115B PRO* 1.3 89.9 - - - +
117B TYR* 1.3 60.4 + - - +
119B GLN* 3.9 11.3 + - - +
120B CYS* 3.2 29.3 + - - -
314B GLY 5.3 0.9 - - - +
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 2.7 39.4 + - - +
43B LEU* 4.2 9.9 - - + -
44B GLY* 3.8 20.4 - - - -
105B LEU* 3.9 13.7 - - - +
113B ILE* 3.7 18.8 - - + -
114B LEU 2.6 15.7 + - - +
116B GLU* 1.3 75.2 - - - +
118B LEU* 1.3 64.4 - - - +
120B CYS* 3.0 10.2 + - + +
121B VAL* 3.0 42.0 + - + +
129B LEU* 4.3 17.0 - - + -
314B GLY 3.4 25.1 - - - +
315B ILE* 3.7 33.1 - - + +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.4 38.4 - - + +
114B LEU 3.0 7.1 + - - +
115B PRO* 3.6 13.2 - - + +
117B TYR* 1.3 83.0 - - - +
119B GLN* 1.3 56.1 - - - +
121B VAL* 3.6 10.7 + - + -
122B LYS* 3.0 38.7 + - + +
129B LEU* 4.9 19.5 - - + +
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Residues in contact with GLN 119 (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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73B CYS* 4.9 1.5 - - + +
74B GLY* 3.1 36.5 - - - +
115B PRO 2.8 17.7 + - - +
116B GLU* 4.1 10.5 + - - +
117B TYR 3.1 0.2 - - - -
118B LEU* 1.3 74.1 - - - +
120B CYS* 1.3 67.9 + - - +
122B LYS* 3.4 12.8 + - + +
123B GLU* 3.1 25.1 + - + +
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Residues in contact with CYS 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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43B LEU* 4.5 19.5 - - + -
70B GLU 4.9 1.3 - - - -
73B CYS* 2.0 52.5 - - - -
116B GLU 3.2 19.7 + - - -
117B TYR* 3.0 13.7 + - + +
119B GLN* 1.3 79.3 - - - +
121B VAL* 1.3 58.1 + - + +
123B GLU* 3.1 2.3 + - - -
124B LEU* 2.8 35.4 + - + +
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Residues in contact with VAL 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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40B MET* 4.4 10.3 - - + -
43B LEU* 5.5 2.0 - - + -
117B TYR* 3.0 52.3 + - + +
118B LEU* 4.0 9.9 - - + +
120B CYS* 1.3 75.0 - - + +
122B LYS* 1.3 61.7 + - - +
125B TYR* 2.6 63.7 + - + +
126B ARG* 5.0 0.4 - - - -
127B GLY 5.0 0.9 - - - +
128B GLY* 4.1 3.8 - - - +
129B LEU* 4.0 26.0 - - + +
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Residues in contact with LYS 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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118B LEU* 3.0 29.8 + - + +
119B GLN* 3.5 12.6 - - + +
121B VAL* 1.3 77.9 - - - +
123B GLU* 1.3 60.7 + - + +
126B ARG* 3.6 52.4 + - + +
127B GLY 5.6 0.4 - - - +
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Residues in contact with GLU 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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73B CYS 2.6 29.5 - - - +
74B GLY* 3.7 11.6 - - - -
76B SER 3.1 23.4 + - - +
77B VAL* 3.4 15.5 + - + +
84B ARG* 3.6 12.5 + - - -
119B GLN* 3.1 17.6 + - + +
120B CYS* 3.9 3.1 - - - +
122B LYS* 1.3 79.9 - - + +
124B LEU* 1.3 70.0 + - + +
126B ARG* 5.1 0.4 - - - -
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Residues in contact with LEU 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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43B LEU* 4.3 20.2 - - + -
73B CYS* 4.3 16.2 - - - -
76B SER 4.6 2.2 - - - +
77B VAL* 4.8 1.1 - - - -
79B VAL* 3.1 42.0 - - + +
80B HIS* 5.2 2.2 - - - +
84B ARG* 3.2 49.8 + - - +
120B CYS* 2.8 21.0 + - - +
123B GLU* 1.3 88.9 - - + +
125B TYR* 1.3 78.7 + - + +
126B ARG 3.7 1.6 - - - -
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Residues in contact with TYR 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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36B SER* 3.6 31.9 - - - -
39B ALA* 3.4 11.3 - - - +
40B MET* 3.5 43.3 - - + -
43B LEU* 3.8 24.2 - - + -
80B HIS* 3.0 30.5 + - - +
83B LEU* 4.7 4.2 - - + +
84B ARG* 4.0 14.3 - - + +
121B VAL* 2.6 25.4 + - + +
124B LEU* 1.3 94.0 - - + +
126B ARG* 1.3 67.9 + - - +
128B GLY* 2.8 16.9 + - - -
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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