Contacts of the helix formed by residues 109 - 119 (chain B) in PDB entry 1SG4
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B VAL* 5.4 0.2 - - + -
63B SER 3.2 13.5 - - - +
64B ALA* 3.6 11.7 - - - +
107B ALA* 3.6 9.6 - - + -
108B CYS* 1.3 88.2 - - - +
110B ALA* 1.3 66.9 + - - +
111B GLY 3.5 0.9 - - - -
112B GLY 2.9 14.9 + - - -
113B CYS 2.9 8.0 + - - -
131B CYS 4.2 1.1 - - - +
133B GLY 3.2 8.3 - - - +
135B ASN* 3.6 13.5 - - - +
169B LEU* 3.7 17.9 - - + -
701B CO8 3.6 40.2 - - + +
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Residues in contact with ALA 110 (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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109B PRO* 1.3 72.9 - - - +
111B GLY* 1.3 58.6 + - - +
113B CYS* 2.9 5.4 + - - +
114B LEU* 2.9 24.7 + - - +
133B GLY 3.1 9.3 + - - -
134B LEU* 3.5 9.2 - - - +
135B ASN* 3.1 17.2 + - - +
136B GLU* 3.5 35.7 - - + +
147B LEU* 4.8 1.0 - - - +
701B CO8 3.5 22.3 - - - -
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Residues in contact with GLY 111 (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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28B LEU* 3.6 18.3 - - - +
65B GLY* 3.4 18.7 - - - -
66B LEU* 4.0 6.7 - - - -
109B PRO 3.2 0.6 + - - -
110B ALA* 1.3 73.6 - - - +
112B GLY* 1.4 61.4 + - - +
114B LEU* 3.1 24.5 + - - +
115B VAL* 3.3 6.4 + - - +
147B LEU* 6.1 0.2 - - - -
701B CO8 3.1 21.2 + - - -
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Residues in contact with GLY 112 (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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62B PHE* 3.8 3.0 - - - -
63B SER* 3.7 30.1 - - - -
65B GLY* 3.5 8.1 - - - -
108B CYS* 3.3 16.2 - - - -
109B PRO 2.9 8.4 + - - -
111B GLY* 1.4 75.8 - - - +
113B CYS* 1.3 58.6 + - - +
115B VAL* 3.0 9.7 + - - +
116B ALA 2.9 22.3 + - - -
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Residues in contact with CYS 113 (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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108B CYS* 3.5 11.1 - - - +
109B PRO 2.9 10.5 + - - +
110B ALA 3.2 10.8 - - - +
112B GLY* 1.3 76.2 - - - +
114B LEU* 1.3 53.7 + - - +
116B ALA* 4.3 1.8 - - - +
117B LEU* 2.7 55.6 + - - +
132B ILE* 3.6 25.8 - - - -
133B GLY* 3.5 27.1 - - - +
134B LEU* 3.6 10.3 - - + -
180B ILE* 4.0 8.5 - - - -
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Residues in contact with LEU 114 (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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28B LEU* 5.7 1.8 - - + -
66B LEU* 5.6 4.0 - - + -
86B VAL* 4.2 15.0 - - + +
89B LEU* 4.6 9.9 - - + -
90B TRP* 4.1 34.9 - - + +
93B LEU* 4.8 1.8 - - + -
110B ALA 2.9 9.2 + - - +
111B GLY* 3.1 19.1 - - - +
113B CYS* 1.3 77.8 - - - +
115B VAL* 1.3 74.1 + - + +
117B LEU* 3.6 1.2 + - - +
118B THR* 3.1 28.9 + - + +
134B LEU* 4.5 1.2 - - - +
146B TRP* 3.6 31.9 - - + -
147B LEU* 3.9 26.2 - - + +
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Residues in contact with VAL 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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20B PHE* 4.3 11.7 - - + -
28B LEU* 4.7 11.9 - - + -
36B LEU* 5.3 4.5 - - + -
54B LEU* 3.6 28.3 - - + -
62B PHE* 4.2 16.4 - - + -
63B SER* 5.8 1.8 - - - -
89B LEU* 4.2 16.8 - - + -
93B LEU* 4.2 18.8 - - + -
102B SER* 4.7 0.2 - - - +
111B GLY 3.7 11.4 - - - +
112B GLY* 3.0 10.1 + - - +
114B LEU* 1.3 77.7 - - + +
116B ALA* 1.3 63.3 + - - +
118B THR* 2.7 22.5 + - - -
119B CYS* 3.5 7.6 - - - -
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Residues in contact with ALA 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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62B PHE* 4.4 2.6 - - + -
102B SER* 3.6 14.4 - - - +
104B ILE* 3.9 27.6 - - + -
108B CYS* 4.2 10.3 - - - -
112B GLY 2.9 14.3 + - - +
113B CYS 3.8 3.1 - - - +
115B VAL* 1.3 76.8 - - - +
117B LEU* 1.3 60.9 + - + +
119B CYS* 3.1 10.2 + - - +
122B ARG* 3.0 31.9 + - - +
132B ILE* 4.2 6.5 - - + -
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Residues in contact with LEU 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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94B TYR* 4.3 1.4 - - - -
113B CYS* 2.7 41.6 + - - +
114B LEU* 4.1 3.4 - - - +
116B ALA* 1.3 72.1 - - + +
118B THR* 1.3 61.0 + - - +
119B CYS 3.7 1.9 - - - +
122B ARG* 3.6 14.7 + - - +
132B ILE* 5.8 0.2 - - + -
134B LEU* 4.2 14.6 - - + -
147B LEU* 4.4 8.3 - - + -
150B THR* 3.6 21.5 - - + +
151B LEU* 4.0 29.8 - - + +
154B THR* 3.7 30.1 + - + +
180B ILE* 3.9 30.7 - - + +
217B ARG* 4.3 5.2 + - - -
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Residues in contact with THR 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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90B TRP* 3.4 35.9 - - + +
93B LEU* 3.2 40.4 - - + +
94B TYR* 3.9 21.5 - - + +
100B LEU* 4.9 1.3 - - - +
114B LEU* 3.1 16.9 + - + +
115B VAL 2.7 18.8 + - - -
117B LEU* 1.3 75.5 - - - +
119B CYS* 1.3 62.6 + - - +
120B ASP* 5.0 0.2 - - - +
150B THR* 4.8 1.1 - - + -
213B LYS* 5.0 1.6 + - - -
217B ARG* 2.8 23.1 + - - -
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Residues in contact with CYS 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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54B LEU* 3.8 21.5 - - - -
100B LEU* 3.4 27.8 - - - +
101B VAL 4.2 0.2 - - - -
102B SER* 3.1 29.4 - - - +
115B VAL 3.5 11.9 - - - -
116B ALA 3.1 11.8 + - - +
118B THR* 1.3 80.8 - - - +
120B ASP* 1.3 61.4 + - - +
121B TYR 3.4 13.7 - - - +
122B ARG* 3.0 16.4 + - - +
217B ARG* 3.1 16.2 + - - -
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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