Contacts of the helix formed by residues 114 - 126 (chain B) in PDB entry 3UMO
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 ASN 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B LYS* 4.0 15.4 - - - +
113B LEU* 1.3 77.0 - - - +
115B GLU* 1.3 64.3 + - - +
116B ASP* 3.2 11.4 + - - +
117B GLU* 2.8 60.6 + - - +
118B PHE* 3.2 19.4 + - - +
143B GLY 5.0 2.5 - - - -
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Residues in contact with GLU 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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114B ASN* 1.3 75.8 - - - +
116B ASP* 1.3 57.1 + - - +
118B PHE* 3.4 7.3 + - - +
119B ARG* 3.0 27.9 + - - +
143B GLY 5.1 9.0 - - - +
145B LYS* 4.7 13.3 + - - +
148B LYS* 5.2 16.6 + - - +
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Residues in contact with ASP 116 (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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114B ASN* 3.2 10.6 + - - +
115B GLU* 1.3 77.0 - - - +
117B GLU* 1.3 63.5 + - - +
119B ARG* 2.6 39.5 + - - +
120B GLN* 3.0 44.4 + - - +
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Residues in contact with GLU 117 (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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83B VAL* 3.9 7.0 - - + +
84B GLU 3.8 17.3 - - - +
85B ALA* 3.3 14.8 - - - +
86B LYS* 2.8 32.4 + - - +
87B ASP 5.3 0.3 + - - -
112B ALA 4.1 2.1 - - - +
113B LEU* 3.5 25.0 - - + +
114B ASN* 2.8 51.0 + - - +
116B ASP* 1.3 74.6 - - - +
118B PHE* 1.3 66.3 + - - +
120B GLN* 3.4 13.3 + - - +
121B LEU* 3.1 28.0 + - - +
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Residues in contact with PHE 118 (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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9B LEU* 4.0 31.4 - - + -
113B LEU* 4.6 8.4 - - + +
114B ASN 3.2 12.5 + - - +
115B GLU* 3.8 9.2 - - - +
117B GLU* 1.3 73.8 - - - +
119B ARG* 1.3 61.2 + - - +
121B LEU* 3.1 8.9 + - + +
122B GLU* 2.9 47.1 + - - +
144B VAL* 3.7 34.1 - - + -
148B LYS* 3.5 56.1 - - + -
149B LEU* 4.2 2.2 - - - -
152B LEU* 3.7 19.7 - - + -
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Residues in contact with ARG 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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115B GLU 3.0 15.8 + - - +
116B ASP* 2.6 37.2 + - - +
118B PHE* 1.3 80.5 - - - +
120B GLN* 1.3 75.3 + - - +
122B GLU* 3.3 9.0 + - + +
123B GLU* 2.9 42.8 + - + +
148B LYS* 5.8 2.2 - - - +
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Residues in contact with GLN 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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83B VAL* 3.7 33.0 - - + +
84B GLU 4.8 5.2 + - - +
116B ASP* 3.0 37.2 + - - +
117B GLU* 3.6 10.6 - - - +
119B ARG* 1.3 91.8 - - - +
121B LEU* 1.3 60.5 + - - +
123B GLU* 3.2 18.0 + - - +
124B GLN* 2.9 30.9 + - + +
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Residues in contact with LEU 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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7B LEU* 4.6 6.1 - - + -
9B LEU* 3.9 23.8 - - + -
58B ILE* 3.9 19.2 - - + +
59B PHE* 3.9 23.1 - - - +
60B PRO* 3.9 24.0 - - + -
83B VAL* 3.6 21.5 - - + -
113B LEU* 3.9 16.8 - - + -
117B GLU 3.1 19.2 + - - +
118B PHE* 3.1 10.3 + - + +
120B GLN* 1.3 76.6 - - - +
122B GLU* 1.3 62.8 + - - +
124B GLN* 3.2 6.1 + - - +
125B VAL* 3.0 26.9 + - - +
152B LEU* 5.0 2.2 - - + -
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Residues in contact with GLU 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 PHE* 2.9 34.9 + - - +
119B ARG* 3.6 8.2 - - + +
120B GLN 3.3 0.2 - - - -
121B LEU* 1.3 76.3 - - - +
123B GLU* 1.3 56.7 + - - +
125B VAL* 3.2 3.5 + - - +
126B LEU* 2.9 44.8 + - + +
148B LYS* 4.6 6.2 + - - +
151B GLN* 4.3 5.4 - - - +
152B LEU* 4.0 38.0 + - + +
155B ALA* 4.0 19.4 - - - +
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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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119B ARG* 2.9 30.4 + - + +
120B GLN* 3.3 19.3 - - - +
122B GLU* 1.3 77.4 - - - +
124B GLN* 1.3 69.2 + - - +
126B LEU* 3.3 8.1 + - - +
127B GLU* 3.2 40.6 + - + +
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Residues in contact with GLN 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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58B ILE* 4.0 25.5 - - + +
81B ALA* 3.9 21.5 - - + +
82B THR 5.2 5.9 + - - +
83B VAL* 4.3 15.8 - - + +
120B GLN 2.9 17.9 + - - +
121B LEU 3.4 8.3 - - - +
123B GLU* 1.3 83.9 + - - +
125B VAL* 1.3 62.6 + - - +
127B GLU* 3.2 41.2 + - - +
128B ILE* 3.9 6.9 + - - +
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Residues in contact with VAL 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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7B LEU* 4.3 27.4 - - + -
58B ILE* 4.2 16.4 - - + -
121B LEU 3.0 17.4 + - - +
122B GLU* 3.2 10.5 + - - +
124B GLN* 1.3 76.5 - - - +
126B LEU* 1.3 62.7 + - + +
128B ILE* 3.1 34.5 + - + +
134B LEU* 3.8 26.7 - - + -
152B LEU* 4.3 13.5 - - + -
156B ALA* 4.3 17.9 - - + -
161B ILE* 3.4 4.3 - - + +
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Residues in contact with LEU 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 GLU* 2.9 36.4 + - + +
123B GLU* 3.3 7.8 + - - +
124B GLN 3.3 0.4 - - - -
125B VAL* 1.3 80.5 - - + +
127B GLU* 1.3 60.0 + - - +
128B ILE 3.2 1.8 - - - -
152B LEU 4.9 1.1 - - - +
155B ALA* 3.9 18.4 - - + -
156B ALA* 3.9 30.5 - - - +
159B GLN* 2.9 44.9 + - - +
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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