Contacts of the helix formed by residues 114 - 126 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A LYS* 4.3 12.9 - - - +
112A ALA 4.3 0.2 - - - -
113A LEU* 1.3 76.6 - - - +
115A GLU* 1.3 65.0 + - - +
116A ASP* 3.2 10.6 + - - +
117A GLU* 2.7 65.6 + - - +
118A PHE* 3.1 19.9 + - - +
143A GLY 4.9 2.7 - - - -
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Residues in contact with GLU 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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114A ASN* 1.3 74.8 - - - +
116A ASP* 1.3 63.3 + - - +
118A PHE* 3.3 7.1 + - - +
119A ARG* 3.1 51.3 + - - +
143A GLY 5.0 9.2 - - - +
145A LYS* 5.3 9.7 + - - +
148A LYS* 6.0 10.4 - - + +
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Residues in contact with ASP 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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114A ASN* 3.2 11.3 + - - +
115A GLU* 1.3 78.7 - - - +
117A GLU* 1.3 58.8 + - - +
119A ARG* 3.2 21.8 + - - +
120A GLN* 3.0 49.9 + - - +
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Residues in contact with GLU 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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83A VAL* 4.1 5.3 - - + +
84A GLU 4.0 14.4 - - - +
85A ALA* 3.3 15.5 - - + +
86A LYS* 2.7 33.6 + - - +
87A ASP 5.3 0.5 + - - -
112A ALA 4.1 2.1 - - - +
113A LEU* 3.6 22.0 - - + +
114A ASN* 2.7 53.3 + - - +
116A ASP* 1.3 75.4 - - - +
118A PHE* 1.3 61.5 + - - +
120A GLN* 3.2 17.3 + - - +
121A LEU* 3.0 27.5 + - - +
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Residues in contact with PHE 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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9A LEU* 3.9 33.2 - - + -
113A LEU* 4.5 4.2 - - + +
114A ASN 3.1 13.6 + - - +
115A GLU* 3.8 9.9 - - - +
116A ASP 3.3 0.2 - - - -
117A GLU* 1.3 76.1 - - - +
119A ARG* 1.3 59.4 + - + +
121A LEU* 3.1 10.1 + - + +
122A GLU* 2.8 36.3 + - - +
144A VAL* 3.7 37.0 - - + -
148A LYS* 3.3 64.6 - - + -
149A LEU* 4.2 3.4 - - + -
152A LEU* 3.7 21.3 - - + -
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Residues in contact with ARG 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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115A GLU* 3.1 37.1 + - - +
116A ASP* 3.6 34.3 + - - +
118A PHE* 1.3 77.0 - - + +
120A GLN* 1.3 57.9 + - - +
122A GLU* 3.3 18.6 + - - +
123A GLU* 2.9 27.7 + - - +
148A LYS* 5.2 15.2 - - - +
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Residues in contact with GLN 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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83A VAL* 3.4 31.2 - - + +
84A GLU 4.8 5.4 + - - +
116A ASP* 3.0 45.0 + - - +
117A GLU* 3.2 18.6 + - - +
119A ARG* 1.3 74.8 - - - +
121A LEU* 1.3 63.1 + - - +
123A GLU* 3.3 17.5 + - - +
124A GLN* 3.2 25.1 + - - +
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Residues in contact with LEU 121 (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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7A LEU* 4.4 8.1 - - + -
9A LEU* 3.8 19.5 - - + -
58A ILE* 4.0 17.8 - - + +
59A PHE* 3.9 25.1 - - - -
60A PRO* 3.9 11.4 - - + -
83A VAL* 3.8 20.4 - - + -
113A LEU* 3.8 33.2 - - + -
117A GLU 3.0 18.5 + - - +
118A PHE* 3.4 10.1 - - + +
120A GLN* 1.3 72.3 - - - +
122A GLU* 1.3 66.0 + - - +
124A GLN* 3.1 6.7 + - - +
125A VAL* 3.1 26.4 + - - +
152A LEU* 4.8 2.9 - - + -
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Residues in contact with GLU 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 PHE* 2.8 25.7 + - - +
119A ARG* 3.4 19.0 - - - +
121A LEU* 1.3 76.7 - - - +
123A GLU* 1.3 61.9 + - - +
125A VAL* 3.2 4.1 + - + +
126A LEU* 3.0 42.8 + - + +
148A LYS* 3.5 21.9 + - - -
151A GLN* 4.0 8.7 - - - +
152A LEU* 3.7 42.9 + - + +
155A ALA* 4.4 5.7 - - + +
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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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119A ARG 2.9 13.8 + - - +
120A GLN* 3.4 20.2 - - - +
121A LEU 3.2 0.2 - - - -
122A GLU* 1.3 75.9 - - - +
124A GLN* 1.3 64.6 + - + +
126A LEU* 3.4 8.1 + - - +
127A GLU* 3.3 36.1 + - + +
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Residues in contact with GLN 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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58A ILE* 4.0 24.0 - - + +
81A ALA* 3.8 24.3 - - + +
82A THR 5.0 6.5 - - - +
83A VAL* 4.3 16.4 - - + -
120A GLN 3.2 15.0 + - - +
121A LEU 3.1 9.5 + - - +
123A GLU* 1.3 79.2 - - - +
125A VAL* 1.3 62.8 + - - +
127A GLU* 3.1 40.9 + - - +
128A ILE* 3.8 7.1 + - - +
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Residues in contact with VAL 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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7A LEU* 4.2 22.2 - - + -
58A ILE* 4.3 13.7 - - + -
121A LEU 3.1 15.4 + - - +
122A GLU* 3.2 9.2 + - - +
124A GLN* 1.3 75.9 - - - +
126A LEU* 1.3 60.8 + - + +
128A ILE* 3.0 35.1 + - + +
134A LEU* 3.6 32.8 - - + -
152A LEU* 4.5 11.9 - - + -
156A ALA* 4.0 21.3 - - + -
161A ILE* 3.4 5.1 - - + +
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Residues in contact with LEU 126 (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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122A GLU* 3.0 26.8 + - + +
123A GLU* 3.4 7.8 + - - +
124A GLN 3.3 0.2 - - - -
125A VAL* 1.3 82.3 - - + +
127A GLU* 1.3 59.0 + - - +
128A ILE 3.3 1.2 - - - +
152A LEU* 5.1 0.7 - - + +
155A ALA* 3.7 34.5 - - + +
156A ALA* 3.8 14.8 - - - +
159A GLN* 3.1 42.2 + - - +
161A ILE* 4.5 0.2 - - + -
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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