Contacts of the helix formed by residues 106 - 124 (chain I) in PDB entry 5T0G
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 PRO 106 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I TYR* 3.9 8.1 - - + +
103I GLU* 4.6 7.2 - - - +
104I PRO 3.5 8.1 - - - +
105I ILE* 1.3 90.2 - - + +
107I CYS* 1.3 65.5 + - - +
108I GLU* 3.2 19.1 + - - +
109I GLN* 3.2 31.2 - - + +
110I LEU* 3.4 18.8 + - - +
140I ASP* 4.5 19.1 - - + +
142I HIS* 5.9 7.2 - - + -
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Residues in contact with CYS 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I MET* 4.0 21.8 - - - -
106I PRO* 1.3 71.2 - - - +
108I GLU* 1.3 70.5 + - - +
110I LEU* 3.2 8.8 - - + +
111I VAL* 2.9 27.7 + - + +
136I TYR* 6.1 2.2 - - + -
137I ILE 4.8 2.5 - - - -
138I GLY* 4.2 27.1 - - - -
139I TRP 4.4 9.0 - - - -
140I ASP* 4.8 1.5 + - - -
146I GLN* 3.0 28.9 - - - +
148I TYR* 3.8 15.3 - - + -
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Residues in contact with GLU 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I PRO* 3.2 14.9 - - - +
107I CYS* 1.3 88.2 + - - +
109I GLN* 1.3 66.0 + - + +
111I VAL* 3.2 2.8 + - - +
112I THR* 3.0 28.3 + - + +
140I ASP* 3.0 7.9 - - - +
142I HIS* 5.7 0.2 - - - +
143I TYR* 3.9 15.2 - - + -
146I GLN* 2.7 28.7 + - - -
148I TYR* 3.8 21.7 - - - +
57J ARG* 4.5 6.0 + - - +
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Residues in contact with GLN 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I TYR* 3.1 30.5 + - - -
105I ILE* 3.2 25.5 - - + +
106I PRO* 3.2 18.2 - - + +
108I GLU* 1.3 78.9 - - + +
110I LEU* 1.3 67.8 + - - +
112I THR* 3.0 10.7 + - - +
113I ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I LEU* 4.1 6.7 - - + -
72I MET* 3.9 31.4 - - + -
90I LEU* 3.9 36.0 - - + +
93I ILE* 4.3 11.1 - - + +
94I ALA* 4.0 23.6 - - + -
105I ILE* 3.7 19.7 - - + +
106I PRO 3.4 10.7 + - - +
107I CYS* 3.2 11.0 - - + +
109I GLN* 1.3 81.6 - - - +
111I VAL* 1.3 66.2 + - + +
113I ALA* 3.0 16.6 + - - +
114I LEU* 3.1 12.0 + - - +
136I TYR* 5.1 9.0 - - + -
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Residues in contact with VAL 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I CYS* 2.9 21.0 + - + +
108I GLU* 3.7 3.1 - - - +
110I LEU* 1.3 79.4 - - + +
112I THR* 1.3 65.5 + - + +
114I LEU* 3.0 6.9 + - - +
115I CYS* 2.9 24.5 + - - -
136I TYR* 3.7 56.1 - - + +
148I TYR* 4.1 21.8 - - + -
149I GLN 4.9 0.9 - - - +
156I TYR* 3.8 29.4 - - + -
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Residues in contact with THR 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I GLU* 3.0 14.7 + - + +
109I GLN* 3.0 22.1 + - - -
111I VAL* 1.3 77.1 - - + +
113I ALA* 1.3 61.0 + - - +
115I CYS* 3.3 8.5 + - - +
116I ASP* 3.0 33.8 + - - +
156I TYR* 4.3 27.8 - - + -
81J ARG* 4.3 15.0 - - - +
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Residues in contact with ALA 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I ILE* 4.6 21.3 - - + -
109I GLN 2.9 15.2 + - - +
110I LEU* 3.0 11.2 + - - +
112I THR* 1.3 77.3 + - - +
114I LEU* 1.3 64.0 + - - +
116I ASP* 3.3 9.2 + - - +
117I ILE* 3.0 28.2 + - + +
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Residues in contact with LEU 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I LEU* 4.1 40.4 - - + +
89I GLU* 4.9 7.4 - - + -
90I LEU* 3.6 34.3 - - + +
110I LEU 3.1 2.4 + - - -
111I VAL 3.0 8.1 + - - +
113I ALA* 1.3 78.6 - - - +
115I CYS* 1.3 64.2 + - - +
117I ILE* 3.0 25.4 + - + -
118I LYS* 2.9 32.8 + - + +
134I LEU* 4.9 7.6 - - + -
136I TYR* 3.3 23.3 - - + +
150I SER* 5.7 0.9 - - - -
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Residues in contact with CYS 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I VAL* 2.9 20.8 + - - +
112I THR* 3.6 10.5 - - - +
113I ALA 3.2 0.2 - - - -
114I LEU* 1.3 77.7 - - - +
116I ASP* 1.3 60.6 + - - +
118I LYS* 3.2 18.9 + - - +
119I GLN* 2.9 27.6 + - - +
136I TYR* 5.8 0.4 - - - -
150I SER* 4.9 7.6 - - - -
154I GLY* 3.2 21.5 - - - +
155I ASN 4.1 2.9 - - - -
156I TYR* 3.6 39.9 - - - -
81J ARG* 4.6 4.9 - - - +
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Residues in contact with ASP 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I THR* 3.0 18.1 + - - +
113I ALA* 3.9 6.4 - - - +
115I CYS* 1.3 72.5 - - - +
117I ILE* 1.3 67.0 + - + +
119I GLN* 3.2 15.6 + - - +
120I ALA* 3.0 22.9 + - - +
81J ARG* 3.1 30.7 + - - +
82J ILE* 4.0 22.9 - - + +
85J ASN* 3.8 17.5 + - - -
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Residues in contact with ILE 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I LEU* 5.4 2.7 - - + -
89I GLU* 4.0 34.1 - - + +
90I LEU* 6.2 0.9 - - - -
93I ILE* 4.6 13.7 - - + -
113I ALA* 3.0 17.7 + - + +
114I LEU* 3.0 25.2 + - + +
116I ASP* 1.3 78.2 - - + +
118I LYS* 1.3 63.1 + - + +
120I ALA* 3.3 12.8 + - - +
121I TYR* 3.2 35.1 - - + +
130I PHE* 5.4 2.5 - - + -
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Residues in contact with LYS 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I LEU* 4.4 16.4 - - + +
114I LEU* 2.9 29.9 + - + +
115I CYS* 3.6 19.5 - - - +
117I ILE* 1.3 75.4 - - + +
119I GLN* 1.3 62.7 + - - +
121I TYR* 3.3 12.6 + - - +
122I THR* 3.2 17.2 + - - +
129I PRO* 5.8 0.7 - - - +
130I PHE* 4.0 36.4 - - + +
132I VAL 4.1 8.1 + - - +
134I LEU* 5.9 0.4 - - - +
150I SER* 3.3 33.0 + - - -
151I ASP 3.0 32.5 + - - +
152I PRO* 4.1 11.1 - - + +
154I GLY* 5.0 1.8 - - - -
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Residues in contact with GLN 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I CYS 2.9 11.3 + - - +
116I ASP* 3.2 22.2 + - - +
118I LYS* 1.3 74.5 - - - +
120I ALA* 1.3 54.5 + - - +
122I THR* 2.3 43.0 + - - +
123I GLN* 2.7 37.8 - - - +
153I SER 4.9 5.4 - - - +
154I GLY* 4.4 12.3 - - - +
78J ALA* 2.4 41.9 + - - +
79J ASP* 3.2 12.9 + - - +
81J ARG* 4.5 0.5 + - - +
82J ILE* 3.4 27.0 - - + +
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Residues in contact with ALA 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ASP 3.0 11.7 + - - +
117I ILE* 3.3 14.4 - - + +
119I GLN* 1.3 76.8 - - - +
121I TYR* 1.3 66.5 + - + +
122I THR 3.0 1.6 + - - -
123I GLN* 3.2 11.5 + - - -
124I PHE* 3.3 44.4 + - + -
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Residues in contact with TYR 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H GLN* 3.6 27.8 - - - -
10I THR* 5.2 1.7 + - - -
117I ILE* 3.2 38.3 - - + +
118I LYS 3.3 7.4 + - - +
119I GLN 3.2 0.4 - - - -
120I ALA* 1.3 78.4 - - + +
122I THR* 1.3 59.1 + - - +
124I PHE* 3.7 14.8 - - - +
127I LYS* 3.6 41.7 + - + +
129I PRO* 4.8 13.4 - - + +
130I PHE* 3.5 31.8 - + + -
3J TYR* 6.0 0.7 - - - -
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Residues in contact with THR 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I THR* 3.6 12.0 + - - +
18I LEU* 6.3 1.3 - - - -
21I VAL* 5.4 11.7 - - + -
118I LYS 3.2 17.0 - - - +
119I GLN* 2.3 34.2 + - - +
121I TYR* 1.3 81.3 - - - +
123I GLN* 1.3 64.6 + - - -
124I PHE 3.4 1.2 + - - -
129I PRO* 4.8 15.3 - - + -
152I PRO 4.1 17.7 - - - +
153I SER 4.9 6.2 + - - +
125J ARG* 2.3 34.1 + - - -
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Residues in contact with GLN 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I THR* 3.8 4.4 - - - +
119I GLN* 2.7 44.7 + - - +
120I ALA* 3.2 4.5 + - - -
122I THR* 1.3 88.3 + - - +
124I PHE* 1.3 73.0 + - + +
79J ASP* 2.6 32.1 + - - -
82J ILE* 5.3 2.5 - - - +
118J TYR* 3.2 26.2 - - - +
124J ARG* 4.0 1.2 + - - -
125J ARG* 3.1 50.6 + - + +
127J PHE* 3.9 9.4 - - + -
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Residues in contact with PHE 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I THR* 4.2 7.2 - - - -
120I ALA* 3.3 41.7 - - + +
121I TYR* 3.7 15.4 - - - +
122I THR 3.4 2.6 + - - -
123I GLN* 1.3 87.4 - - + +
125I GLY* 1.3 60.9 + - - +
126I GLY 3.4 4.1 + - - -
127I LYS* 4.4 2.8 + - - +
3J TYR* 4.0 25.8 - + + -
7J ILE* 6.4 0.2 - - - -
118J TYR* 5.7 1.1 - + - -
123J GLY* 3.0 31.6 - - - +
124J ARG* 4.6 17.0 - - - -
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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