Contacts of the helix formed by residues 118 - 130 (chain A) in PDB entry 3SI5
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 ASP 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.7 5.1 - - - +
114A ARG 5.0 1.9 + - - +
115A TYR* 2.8 32.0 + - + +
116A TYR 5.1 1.0 - - - +
117A SER* 1.3 77.8 - - - +
119A PRO* 1.4 70.7 - - - +
120A ARG* 2.7 68.3 + - - +
121A PHE* 3.1 14.9 + - + +
122A LEU* 3.2 11.6 + - - +
151A LEU* 4.2 1.3 - - - +
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Residues in contact with PRO 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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117A SER 3.5 8.7 - - - +
118A ASP* 1.4 90.7 - - - +
120A ARG* 1.3 58.2 + - + +
121A PHE 3.3 0.2 - - - -
122A LEU* 3.7 5.9 - - + +
123A ASN* 3.0 27.4 + - - +
151A LEU* 4.0 23.8 - - + -
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Residues in contact with ARG 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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73A ASP* 2.7 43.2 + - - -
75A LEU* 3.5 26.0 - - + +
76A ASP* 3.8 21.0 + - - +
79A ASP* 3.8 36.7 - - - +
115A TYR* 3.7 3.0 - - - -
118A ASP* 2.7 36.1 + - - +
119A PRO* 1.3 75.8 - - + +
121A PHE* 1.3 64.1 + - - +
123A ASN* 3.4 9.9 - - - +
124A LEU* 3.3 25.1 + - - +
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Residues in contact with PHE 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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75A LEU* 3.6 11.3 - - + +
106A VAL* 5.8 3.4 - - - -
109A LEU* 3.9 39.5 - - + -
110A GLN* 5.1 2.2 - - - -
111A GLY 5.2 0.2 - - - -
115A TYR* 3.3 39.5 - + + +
116A TYR* 3.6 32.8 - + - -
118A ASP 3.1 10.0 + - - +
120A ARG* 1.3 76.9 - - - +
122A LEU* 1.3 66.6 + - - +
124A LEU* 3.0 27.3 + - + +
125A TRP* 3.3 45.7 + + - -
147A ILE* 3.7 23.8 - - + -
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Residues in contact with LEU 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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116A TYR 6.1 0.2 - - - +
118A ASP 3.2 8.7 + - - +
119A PRO* 3.7 11.4 - - + +
121A PHE* 1.3 77.9 - - - +
123A ASN* 1.3 66.1 + - - +
125A TRP* 3.0 10.0 + - - +
126A LEU* 2.9 42.4 + - + +
142A LEU* 3.6 27.6 - - + -
147A ILE* 4.9 3.8 - - + -
148A GLY* 4.5 9.9 - - - -
151A LEU* 3.8 23.1 - - + -
153A GLN* 4.0 14.1 - - + -
154A PHE* 3.7 37.5 - - + +
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Residues in contact with ASN 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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79A ASP* 4.6 9.5 - - - +
82A ILE* 4.7 5.5 - - - +
119A PRO 3.0 19.1 + - - +
120A ARG* 3.4 12.4 - - - +
122A LEU* 1.3 76.9 - - - +
124A LEU* 1.3 65.9 + - - +
126A LEU* 3.8 9.9 - - - +
127A LYS* 2.9 67.1 + - - +
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Residues in contact with LEU 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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75A LEU* 3.9 23.3 - - + -
78A TRP* 4.8 7.6 - - + +
79A ASP* 5.2 2.9 - - - +
82A ILE* 3.8 30.1 - - + -
102A LEU* 3.8 17.2 - - + +
105A ALA* 3.8 32.8 - - + +
106A VAL* 4.4 15.5 - - + +
109A LEU* 4.2 10.5 - - + -
120A ARG 3.3 12.1 + - - +
121A PHE* 3.0 17.2 + - + +
123A ASN* 1.3 82.5 - - - +
125A TRP* 1.3 58.5 + - + +
128A LEU* 2.9 29.5 + - - +
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Residues in contact with TRP 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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106A VAL* 3.4 41.1 - - + +
110A GLN* 5.5 6.5 - - + -
121A PHE* 3.3 59.0 + + - -
122A LEU 3.0 6.5 + - - +
124A LEU* 1.3 76.9 - - + +
126A LEU* 1.3 55.6 + - - +
128A LEU* 3.2 7.5 + - + +
129A GLY* 2.8 31.9 + - - -
138A MET* 3.6 11.6 - - + +
141A TYR* 3.6 26.5 - + - -
142A LEU* 3.5 37.9 - - + -
147A ILE* 4.0 16.7 - - + +
215X PHE* 3.9 26.2 - + - -
218X PHE* 4.5 3.6 - + - -
219X ILE* 4.2 9.2 - - + -
222X LEU* 4.7 2.2 - - + -
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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 LEU* 2.9 54.7 + - + +
123A ASN* 3.8 9.4 - - - +
125A TRP* 1.3 72.9 - - - +
127A LYS* 1.3 67.0 + - + +
129A GLY* 3.2 1.7 + - - -
130A ARG* 3.2 23.4 + - - +
138A MET* 4.1 8.9 - - + +
139A TYR* 3.5 39.2 + - + +
142A LEU* 4.6 0.9 - - + -
153A GLN* 4.1 13.0 - - + +
154A PHE* 4.9 3.1 - - + -
157A SER* 3.6 22.0 - - - +
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Residues in contact with LYS 127 (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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82A ILE* 3.8 18.8 - - + -
86A GLU* 2.9 40.9 + - - +
98A MET* 4.9 4.7 - - + -
102A LEU* 3.7 24.9 - - + +
123A ASN* 2.9 52.8 + - - +
126A LEU* 1.3 78.1 - - + +
128A LEU* 1.3 63.5 + - - +
130A ARG* 3.5 15.8 + - - +
131A LEU* 3.8 8.5 + - - +
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Residues in contact with LEU 128 (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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102A LEU* 3.7 41.0 - - + +
103A GLU* 4.1 8.3 - - + +
106A VAL* 4.0 10.1 - - + -
124A LEU 2.9 18.0 + - - +
125A TRP* 3.5 8.7 - - + +
127A LYS* 1.3 75.1 - - - +
129A GLY* 1.3 59.5 + - - +
131A LEU* 2.9 24.9 + - - +
132A CYS* 3.4 29.5 - - - -
138A MET* 5.2 0.2 - - + -
213X ILE* 4.7 14.6 - - + -
215X PHE* 4.0 22.2 - - + -
218X PHE* 3.9 27.1 - - + -
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Residues in contact with GLY 129 (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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125A TRP 2.8 20.5 + - - -
126A LEU 3.2 3.0 + - - -
128A LEU* 1.3 74.0 - - - +
130A ARG* 1.3 55.0 + - - +
132A CYS* 3.0 30.9 + - - +
135A PRO* 3.5 20.2 - - - +
138A MET* 3.8 26.7 - - - -
139A TYR* 6.1 0.2 - - - -
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Residues in contact with ARG 130 (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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126A LEU 3.2 11.3 + - - +
127A LYS* 3.8 11.9 - - - +
128A LEU 3.3 0.2 - - - -
129A GLY* 1.3 74.7 - - - +
131A LEU* 1.3 62.8 + - + +
132A CYS 3.4 2.9 + - - +
135A PRO* 4.8 7.0 - - - +
212X LYS* 3.8 15.2 + - - -
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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