Contacts of the helix formed by residues 112 - 129 (chain i) in PDB entry 5GAD
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 GLY 112 (chain i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110i GLY 3.2 1.2 - - - -
111i ALA* 1.3 80.3 - - - +
113i LYS* 1.3 57.3 + - - +
114i THR 3.5 2.0 - - - -
115i THR* 3.6 2.6 + - - -
116i SER* 2.7 38.4 + - - -
220i VAL* 4.1 3.1 - - - -
248i THR* 4.7 0.2 - - - -
1400i GNP 2.8 42.0 + - - -
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Residues in contact with LYS 113 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105i MET* 3.8 8.4 - - + +
106i ALA* 3.5 28.9 - - - -
107i GLY* 3.5 2.7 - - - +
108i LEU 2.8 26.7 + - - -
111i ALA* 3.9 0.4 - - + -
112i GLY* 1.3 69.7 - - - +
114i THR* 1.3 59.1 + - - +
116i SER* 3.1 4.1 + - - -
117i VAL* 2.9 34.0 + - - +
190i ASP* 3.6 11.2 - - - +
191i THR* 3.2 24.7 - - - +
193i GLY* 3.4 17.7 - - - +
220i VAL* 3.5 32.1 - - + -
1400i GNP 2.7 46.6 + - - +
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Residues in contact with THR 114 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113i LYS* 1.3 74.9 - - - +
115i THR* 1.3 63.0 + - - +
117i VAL* 3.4 10.1 + - - +
118i GLY 3.4 8.7 + - - -
144i ALA* 4.8 3.3 + - - +
147i GLN* 3.7 33.7 + - + +
148i LEU* 4.3 17.5 - - + +
151i LEU* 3.6 15.5 - - + +
190i ASP* 2.6 26.9 + - - +
1400i GNP 2.8 15.5 + - - -
1401i MG 2.1 31.6 - - - -
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Residues in contact with THR 115 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112i GLY 3.8 0.9 - - - -
113i LYS 3.3 0.2 - - - -
114i THR* 1.3 74.6 - - - +
116i SER* 1.3 61.3 + - - +
118i GLY* 3.4 3.5 + - - -
119i LYS* 3.1 44.4 + - + +
147i GLN* 4.6 5.4 + - - -
151i LEU* 4.0 14.0 - - + +
277i GLU 4.2 15.9 - - - +
278i LYS 5.4 0.7 - - - +
279i THR* 6.1 1.1 - - + +
1400i GNP 2.5 67.1 + - + +
333l ARG* 5.6 0.5 - - - -
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Residues in contact with SER 116 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105i MET* 3.5 25.6 - - - -
112i GLY 2.7 22.7 + - - -
113i LYS 3.5 0.7 - - - -
115i THR* 1.3 74.0 - - - +
117i VAL* 1.3 66.2 + - - +
119i LYS* 3.2 14.8 + - - +
120i LEU* 2.9 30.9 + - - +
220i VAL* 4.2 1.1 - - - +
246i VAL* 4.4 8.2 - - - +
248i THR* 3.6 21.3 - - - +
282i LEU* 5.7 2.8 - - - +
1400i GNP 5.0 2.1 + - - -
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Residues in contact with VAL 117 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105i MET* 3.4 24.7 - - + +
113i LYS 2.9 19.0 + - - +
114i THR 3.5 8.3 - - - +
115i THR 3.3 0.2 - - - -
116i SER* 1.3 76.6 - - - +
118i GLY* 1.3 56.9 + - - +
120i LEU* 4.5 7.0 - - - -
121i GLY* 3.0 22.9 + - - -
134i VAL* 4.2 7.3 - - + +
148i LEU* 4.2 18.8 - - + -
188i LEU* 3.1 42.2 - - + +
189i VAL 4.5 0.7 - - - -
190i ASP* 3.5 28.9 - - + +
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Residues in contact with GLY 118 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114i THR 3.4 5.7 + - - -
115i THR 3.4 6.3 + - - -
116i SER 3.3 0.4 - - - -
117i VAL* 1.3 76.0 - - - +
119i LYS* 1.3 59.7 - - - +
121i GLY* 3.4 2.7 + - - -
122i LYS* 3.0 28.6 + - - +
134i VAL* 6.0 2.5 - - - -
148i LEU* 5.2 2.9 - - - +
151i LEU* 5.0 14.8 - - - +
152i ALA* 6.3 0.4 - - - -
155i VAL* 3.7 20.7 - - - +
279i THR* 5.1 4.5 - - - -
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Residues in contact with LYS 119 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115i THR* 3.1 34.7 + - + +
116i SER* 3.2 16.9 + - - +
118i GLY* 1.3 71.4 - - - +
120i LEU* 1.3 61.6 + - - +
122i LYS* 3.3 3.1 + - - +
123i PHE* 2.9 30.1 + - - +
274i GLY* 3.7 13.7 - - - -
276i GLY 2.7 30.2 + - - -
278i LYS 3.4 13.2 - - - +
279i THR* 3.4 26.5 - - - +
281i ALA* 3.8 3.8 - - - +
282i LEU* 3.6 35.2 - - + +
1400i GNP 3.1 22.6 + - - -
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Residues in contact with LEU 120 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95i LEU* 5.7 2.0 - - + -
103i VAL* 5.4 0.7 - - + -
105i MET* 3.8 31.4 - - + -
116i SER* 2.9 20.5 + - - +
117i VAL* 3.6 7.2 - - - +
119i LYS* 1.3 75.5 - - - +
121i GLY* 1.3 64.4 + - - +
123i PHE* 4.4 0.4 - - - -
124i LEU* 2.9 41.0 + - + +
188i LEU* 3.6 24.9 - - + -
218i LEU* 4.4 9.9 - - + -
246i VAL* 5.4 2.2 - - + -
272i PHE* 3.5 30.7 - - + -
282i LEU* 3.4 27.1 - - + -
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Residues in contact with GLY 121 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117i VAL 3.0 11.8 + - - -
118i GLY* 3.4 5.6 + - - -
119i LYS 3.2 0.2 - - - -
120i LEU* 1.3 76.3 - - - +
122i LYS* 1.3 55.4 + - - +
124i LEU* 5.2 0.2 - - - -
125i ARG* 2.9 31.4 + - - +
132i VAL* 4.3 15.3 - - - +
134i VAL* 5.5 1.3 - - - -
155i VAL* 5.3 0.7 - - - -
157i VAL* 4.2 14.2 - - - +
188i LEU* 3.3 15.4 - - - +
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Residues in contact with LYS 122 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118i GLY 3.0 16.5 + - - +
119i LYS 3.7 4.3 - - - +
121i GLY* 1.3 74.4 - - - +
123i PHE* 1.3 65.3 + - - +
125i ARG* 3.1 12.8 + - + +
126i GLU* 2.9 50.2 + - + +
154i GLN 5.7 0.4 + - - -
155i VAL* 4.1 37.9 + - + +
279i THR* 4.3 20.2 - - - +
280i GLU* 5.1 17.0 - - + -
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Residues in contact with PHE 123 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94i ASN* 4.6 10.1 - - - -
119i LYS 2.9 18.3 + - - +
120i LEU* 3.8 2.9 - - + +
122i LYS* 1.3 77.2 - - - +
124i LEU* 1.3 80.1 + - + +
126i GLU* 3.1 14.8 + - - +
127i LYS* 2.9 59.5 + - + +
272i PHE* 4.2 22.2 - + - -
282i LEU* 4.0 28.3 - - + -
284i PRO* 4.4 28.3 - - + -
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Residues in contact with LEU 124 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95i LEU* 6.3 3.4 - - + -
103i VAL* 6.4 1.6 - - + -
120i LEU* 2.9 34.9 + - + +
121i GLY* 4.4 1.3 - - - +
123i PHE* 1.3 94.1 - - + +
125i ARG* 1.3 61.0 + - - +
127i LYS* 4.3 2.2 - - + +
128i HIS* 2.9 74.0 + - + +
129i LYS 4.0 0.2 + - - -
130i LYS 4.7 0.9 + - - +
132i VAL* 5.0 6.4 - - + +
186i VAL* 3.6 31.4 - - + -
188i LEU* 5.4 1.8 - - + -
272i PHE* 5.6 4.9 - - + -
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Residues in contact with ARG 125 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121i GLY 2.9 21.9 + - - +
122i LYS* 3.1 14.8 + - + +
124i LEU* 1.3 79.2 - - - +
126i GLU* 1.3 63.2 + - + +
129i LYS* 3.8 15.1 + - - -
130i LYS 2.9 32.0 + - - +
131i LYS* 4.1 15.8 - - - +
132i VAL* 4.7 7.4 - - + +
155i VAL 4.8 10.8 - - - +
156i GLY 4.3 16.3 + - - +
157i VAL* 4.8 7.9 - - + -
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Residues in contact with GLU 126 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122i LYS* 2.9 44.0 + - + +
123i PHE* 3.1 14.4 + - - +
125i ARG* 1.3 80.7 - - + +
127i LYS* 1.3 72.4 + - + +
129i LYS* 4.1 10.6 + - - +
280i GLU* 5.7 3.5 - - - +
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Residues in contact with LYS 127 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123i PHE* 2.9 52.6 + - + +
124i LEU* 4.7 1.6 - - + -
126i GLU* 1.3 86.1 - - + +
128i HIS* 1.3 72.4 + - + +
129i LYS* 3.6 7.4 + - - +
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Residues in contact with HIS 128 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95i LEU 5.9 0.6 + - - -
97i ALA* 4.1 27.1 - - + +
124i LEU* 2.9 56.8 + - + +
127i LYS* 1.3 83.8 - - + +
129i LYS* 1.3 69.3 + - - +
130i LYS* 3.3 26.7 + - + +
132i VAL* 6.4 0.9 - - + -
185i ASP* 4.7 1.0 + - - -
186i VAL* 3.4 25.7 - - + +
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Residues in contact with LYS 129 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125i ARG* 3.8 14.7 + - - -
126i GLU 4.4 8.1 - - - +
127i LYS 3.4 8.4 - - - +
128i HIS* 1.3 80.7 - - - +
130i LYS* 1.3 70.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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