Contacts of the helix formed by residues 114 - 125 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PRO 3.7 2.0 + - - -
113A ILE* 1.3 70.9 - - - +
115A PRO* 1.3 68.4 - - + +
116A GLU* 3.1 54.1 - - + +
117A TYR* 2.9 30.7 + - - +
118A LEU 3.4 4.2 + - - -
313A SER 3.9 17.7 - - - +
314A GLY* 3.9 17.5 - - - +
315A ILE 2.6 24.5 + - - +
316A SER* 4.0 6.9 - - - +
317A SER* 5.0 7.9 - - - +
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Residues in contact with PRO 115 (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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113A ILE 3.1 10.5 - - - +
114A LEU* 1.3 84.7 - - + +
116A GLU* 1.3 63.3 + - - +
117A TYR 3.4 0.2 + - - -
118A LEU* 3.6 14.5 + - + +
119A GLN* 3.5 19.8 + - - +
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Residues in contact with GLU 116 (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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71A ALA* 4.8 10.6 - - - +
73A CYS* 5.2 10.9 - - + +
114A LEU* 3.1 19.9 - - + +
115A PRO* 1.3 80.4 - - - +
117A TYR* 1.3 62.0 + - - +
119A GLN* 3.7 6.5 + - - +
120A CYS* 3.2 20.1 + - + +
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Residues in contact with TYR 117 (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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40A MET* 2.9 30.6 + - - +
43A LEU* 3.9 8.7 - - + -
44A GLY* 3.9 18.4 - - - -
105A LEU* 3.8 17.6 - - + +
113A ILE* 4.4 7.9 - - + -
114A LEU* 2.9 13.5 + - - +
116A GLU* 1.3 78.2 - - - +
118A LEU* 1.3 60.1 + - - +
120A CYS* 2.6 38.3 + - + +
121A VAL* 2.9 33.0 + - + +
129A LEU* 4.6 14.6 - - + -
314A GLY 3.7 25.4 - - - +
315A ILE* 3.7 38.9 - - + +
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Residues in contact with LEU 118 (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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113A ILE* 3.6 32.8 - - + +
114A LEU 3.4 2.9 + - - +
115A PRO* 3.9 15.3 - - + +
116A GLU 3.5 0.2 - - - -
117A TYR* 1.3 78.2 - - + +
119A GLN* 1.3 57.4 + - - +
121A VAL* 3.1 10.7 - - + +
122A LYS* 2.9 31.9 + - - +
129A LEU* 3.9 29.6 - - + +
131A PRO* 6.4 0.2 - - + -
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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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73A CYS 5.1 1.1 - - - +
74A GLY* 3.6 28.6 - - - +
115A PRO 3.5 9.6 + - - +
116A GLU* 3.7 11.0 - - + +
117A TYR 3.1 0.4 - - - -
118A LEU* 1.3 79.0 - - - +
120A CYS* 1.3 63.4 + - - +
122A LYS* 3.3 17.2 + - - +
123A GLU* 3.1 25.3 + - - +
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Residues in contact with CYS 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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43A LEU* 3.1 34.1 - - - -
73A CYS* 2.0 59.7 + - + +
74A GLY* 4.1 6.5 - - - +
116A GLU* 3.2 13.9 + - + +
117A TYR* 2.6 27.1 + - + +
119A GLN* 1.3 77.4 - - - +
121A VAL* 1.3 59.7 + - - -
123A GLU* 3.2 1.2 + - - +
124A LEU* 3.2 17.5 + - - +
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Residues in contact with VAL 121 (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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40A MET* 4.4 15.7 - - + -
43A LEU* 5.0 1.3 - - + -
117A TYR* 2.9 52.5 + - + +
118A LEU* 3.1 23.3 - - + +
120A CYS* 1.3 72.8 - - + +
122A LYS* 1.3 64.0 + - + +
125A TYR* 2.7 43.8 + - - +
128A GLY* 4.5 12.1 - - - -
129A LEU* 4.3 22.7 - - + +
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Residues in contact with LYS 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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118A LEU 2.9 19.8 + - - +
119A GLN* 3.4 21.8 - - - +
120A CYS 3.2 0.2 - - - -
121A VAL* 1.3 79.9 - - + +
123A GLU* 1.3 65.5 + - + +
125A TYR 3.8 9.2 - - - +
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Residues in contact with GLU 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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74A GLY* 3.1 40.5 - - - +
75A THR* 4.7 7.7 - - - +
76A SER 4.9 2.3 + - - +
77A VAL* 4.6 17.2 - - - +
84A ARG* 4.0 10.8 + - - -
119A GLN* 3.1 18.2 + - - +
120A CYS 3.9 0.9 - - - +
121A VAL 3.1 0.2 - - - -
122A LYS* 1.3 84.2 + - + +
124A LEU* 1.3 69.5 + - + +
125A TYR 3.8 0.2 - - - -
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Residues in contact with LEU 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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43A LEU* 4.1 11.7 - - + -
73A CYS* 3.0 33.0 - - - -
74A GLY 4.9 0.4 - - - +
75A THR 5.3 1.1 - - - +
76A SER 4.5 8.7 - - - +
77A VAL* 5.7 1.3 - - - -
79A VAL* 3.6 47.6 - - + +
80A HIS* 5.0 1.8 - - - +
84A ARG* 2.4 48.0 + - - +
88A ASN* 5.1 0.2 - - - +
120A CYS 3.2 8.0 + - - +
123A GLU* 1.3 91.3 - - + +
125A TYR* 1.3 82.2 + - + +
401A SO4 4.4 3.1 + - - -
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Residues in contact with TYR 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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36A SER* 3.5 27.3 - - - -
39A ALA* 3.5 11.4 - - - +
40A MET* 3.9 43.3 - - + -
43A LEU* 3.9 23.3 - - + -
80A HIS* 2.8 31.7 + - - +
83A LEU* 5.3 1.8 - - + +
84A ARG* 4.3 10.9 - - + +
121A VAL* 2.7 31.9 + - - +
122A LYS* 3.8 10.9 - - - +
124A LEU* 1.3 96.3 - - + +
126A ARG* 1.3 64.8 + - - +
128A GLY* 4.4 7.5 + - - +
401A SO4 3.8 20.0 - - - +
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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