Contacts of the helix formed by residues 108 - 124 (chain Q) in PDB entry 3SDI
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 THR 108 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Q HIS* 5.1 2.7 - - + -
106Q PRO 3.6 2.8 + - - +
107Q VAL* 1.3 78.9 - - - +
109Q VAL* 1.3 64.6 + - - +
110Q GLU* 3.7 10.9 + - - +
111Q TYR* 3.0 27.8 + - + +
112Q LEU* 3.2 17.5 + - - +
142Q ASP* 3.6 27.4 - - + +
143Q PRO* 4.5 6.5 - - + -
70Y GLU* 5.3 1.4 + - - +
72Y GLU* 6.0 1.8 - - - +
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Residues in contact with VAL 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Q VAL* 4.2 14.1 - - + -
107Q VAL 5.3 0.2 - - - +
108Q THR* 1.3 68.9 - - - +
110Q GLU* 1.3 64.8 + - - +
112Q LEU* 3.4 6.7 + - - +
113Q THR* 3.0 27.5 + - - -
138Q ILE* 3.7 31.6 - - + +
139Q ALA 4.2 1.3 - - - -
140Q GLY* 3.7 42.8 - - - +
141Q PHE 3.7 9.0 - - - +
142Q ASP* 3.1 16.6 + - - +
147Q LYS* 3.9 16.8 - - + -
149Q TYR* 4.3 5.4 - - + -
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Residues in contact with GLU 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108Q THR* 3.2 9.2 + - - +
109Q VAL* 1.3 80.3 - - - +
111Q TYR* 1.3 57.2 + - - +
113Q THR* 3.3 3.6 + - - -
114Q ARG* 2.9 58.8 + - - -
142Q ASP* 4.6 1.6 + - - +
147Q LYS* 5.8 1.3 - - + +
149Q TYR* 3.3 41.4 - - + +
157Q TYR* 3.5 16.1 + - + -
65R GLU* 5.6 1.6 - - - +
70Y GLU* 4.9 1.0 - - - +
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Residues in contact with TYR 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Q GLU* 3.0 34.8 + - + -
99Q HIS* 3.8 31.4 - + - +
107Q VAL* 3.7 19.5 - - + -
108Q THR* 3.0 28.3 + - + +
110Q GLU* 1.3 79.2 + - - +
112Q LEU* 1.3 60.8 + - - +
114Q ARG* 3.4 22.9 + - - +
115Q TYR* 2.9 30.9 + + + +
70Y GLU* 3.5 35.9 - - - +
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Residues in contact with LEU 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Q ILE* 4.0 27.1 - - + -
74Q VAL* 4.5 8.5 - - + -
76Q LEU* 5.1 0.4 - - + -
92Q ALA* 3.8 31.2 - - + +
95Q GLU* 4.8 7.4 - - + -
96Q ALA* 4.7 3.4 - - + +
107Q VAL* 4.1 26.2 - - + -
108Q THR 3.2 12.4 + - - +
109Q VAL* 3.8 6.5 - - - +
111Q TYR* 1.3 79.3 - - - +
113Q THR* 1.3 64.4 + - - +
115Q TYR* 3.8 5.3 - - + +
116Q VAL* 3.2 32.2 + - + +
138Q ILE* 4.3 20.2 - - + -
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Residues in contact with THR 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Q VAL 3.0 18.1 + - - -
110Q GLU* 3.5 5.6 - - - -
112Q LEU* 1.3 75.0 - - - +
114Q ARG* 1.3 57.8 + - - +
115Q TYR 3.1 0.3 + - - -
116Q VAL* 3.1 3.3 + - - +
117Q ALA* 2.7 32.9 + - - +
138Q ILE* 3.5 22.7 - - + +
149Q TYR* 3.4 33.7 - - + +
151Q THR* 3.8 18.2 - - + -
157Q TYR* 3.5 26.7 - - + -
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Residues in contact with ARG 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110Q GLU* 2.9 44.3 + - - +
111Q TYR* 3.7 21.7 - - - +
113Q THR* 1.3 75.8 - - - +
115Q TYR* 1.3 58.5 + - - +
117Q ALA* 3.9 1.1 - - - +
118Q GLY* 2.9 25.3 + - - -
157Q TYR* 3.7 33.5 + - + +
86R ARG* 5.4 11.9 - - + +
69Y ARG* 3.7 23.6 + - - +
70Y GLU* 3.0 40.2 + - - +
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Residues in contact with TYR 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91Q LYS* 3.5 42.6 + - + +
92Q ALA* 4.3 3.1 - - - -
95Q GLU* 3.7 44.7 + - + +
111Q TYR* 2.9 25.1 + + + +
112Q LEU* 3.8 9.9 - - + +
113Q THR 3.1 0.2 - - - -
114Q ARG* 1.3 77.6 - - - +
116Q VAL* 1.3 73.3 + - + +
118Q GLY* 3.0 12.9 + - - -
119Q VAL* 3.1 37.4 + - + +
122Q ARG* 5.1 9.9 + - - -
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Residues in contact with VAL 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Q LEU* 4.6 5.8 - - + -
88Q LEU* 4.5 22.2 - - + +
92Q ALA* 3.9 27.4 - - + -
112Q LEU* 3.2 22.6 + - + +
113Q THR 3.1 3.9 + - - +
115Q TYR* 1.3 75.8 - - + +
117Q ALA* 1.3 67.4 + - - +
119Q VAL* 3.0 19.7 + - + +
120Q GLN* 3.1 29.3 + - - +
136Q THR* 4.3 10.8 - - + +
138Q ILE* 4.3 10.1 - - + -
151Q THR* 4.1 9.6 - - + +
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Residues in contact with ALA 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113Q THR 2.7 21.7 + - - +
114Q ARG 3.9 2.7 - - - +
116Q VAL* 1.3 72.1 - - - +
118Q GLY* 1.3 56.7 + - - +
120Q GLN* 3.3 11.9 + - - +
121Q GLN* 2.9 26.6 + - - +
151Q THR* 4.1 4.7 - - + +
155Q GLY* 3.4 31.0 - - - +
157Q TYR* 3.5 30.3 - - + -
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Residues in contact with GLY 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114Q ARG 2.9 16.8 + - - -
115Q TYR 3.0 5.1 + - - -
117Q ALA* 1.3 75.8 - - - +
119Q VAL* 1.3 57.5 + - - +
121Q GLN* 3.4 8.5 + - - +
122Q ARG* 2.9 42.4 + - - +
86R ARG* 6.0 7.2 - - - -
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Residues in contact with VAL 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q LEU* 3.8 21.5 - - + -
91Q LYS* 4.2 20.2 - - + +
115Q TYR* 3.1 47.5 + - + +
116Q VAL* 3.0 9.1 + - + +
118Q GLY* 1.3 75.2 - - - +
120Q GLN* 1.3 63.9 + - - +
122Q ARG* 3.2 25.8 + - - +
123Q TYR* 3.1 43.2 - - + -
132Q PHE* 4.2 0.9 - - + -
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Residues in contact with GLN 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q LEU* 3.7 34.4 - - + +
116Q VAL* 3.1 15.6 + - - +
117Q ALA* 3.7 6.3 - - - +
119Q VAL* 1.3 73.6 - - - +
121Q GLN* 1.3 65.4 + - - +
123Q TYR* 3.2 14.0 + - - +
124Q THR* 3.4 13.5 + - - +
132Q PHE* 4.0 19.9 + - + +
134Q VAL* 2.9 29.7 + - - +
151Q THR* 2.8 34.1 + - - -
152Q GLU 3.6 15.4 + - - +
153Q PRO* 3.7 17.1 - - + +
155Q GLY* 4.4 0.2 - - - -
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Residues in contact with GLN 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117Q ALA 2.9 17.2 + - - +
118Q GLY* 3.5 10.3 + - - +
119Q VAL 3.3 0.2 - - - -
120Q GLN* 1.3 76.5 - - - +
122Q ARG* 1.3 66.4 + - - +
124Q THR* 2.8 32.8 + - - +
125Q GLN* 3.0 27.5 + - - +
154Q SER 3.7 15.5 - - - +
155Q GLY* 3.9 4.6 - - - +
83R ALA* 3.3 38.1 - - + +
84R ASP* 2.9 22.2 - - - +
86R ARG* 5.9 2.2 - - + +
87R SER* 5.7 6.1 - - - -
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Residues in contact with ARG 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Q LYS* 6.2 0.2 - - - +
115Q TYR* 5.1 9.9 + - - -
118Q GLY* 2.9 30.8 + - - +
119Q VAL* 3.2 31.8 + - - +
121Q GLN* 1.3 85.1 - - - +
123Q TYR* 1.3 61.0 + - + +
124Q THR 3.2 0.4 - - - -
125Q GLN* 3.3 14.7 + - + +
126Q SER* 2.7 33.8 + - - +
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Residues in contact with TYR 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P GLN* 3.7 28.8 + - + -
126P HIS* 5.0 10.7 + + - -
13Q SER* 4.3 0.7 + - - -
87Q ILE* 4.9 2.6 - - - +
91Q LYS* 3.5 24.3 + - - -
119Q VAL* 3.1 32.1 - - + +
120Q GLN 3.2 10.3 + - - +
122Q ARG* 1.3 84.8 - - + +
124Q THR* 1.3 61.6 + - - +
125Q GLN 3.3 0.8 + - - -
126Q SER* 4.5 0.6 + - - -
129Q VAL* 3.5 44.1 - - + +
130Q ARG 3.8 11.2 - - - +
131Q PRO* 3.8 17.4 - - + +
132Q PHE* 3.5 34.3 - + + -
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Residues in contact with THR 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Q SER* 3.1 24.6 - - - -
24Q VAL* 3.8 25.6 - - + -
120Q GLN 3.4 9.4 - - - +
121Q GLN* 2.8 18.7 + - - +
123Q TYR* 1.3 79.2 - - - +
125Q GLN* 1.3 55.3 + - - +
126Q SER 3.9 0.2 - - - -
131Q PRO* 4.5 5.8 - - + -
153Q PRO 3.3 26.9 - - - +
154Q SER* 4.0 12.0 + - - +
84R ASP* 4.3 1.0 + - - -
130R ARG* 2.8 40.0 + - - -
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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
------------------------------------------------------------
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