Contacts of the helix formed by residues 107 - 120 (chain A) in PDB entry 3LOC
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 TYR 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ILE* 3.9 18.6 - - + +
75A ILE* 4.3 33.4 - - + +
103A VAL* 2.7 34.1 + - + +
106A ASP* 1.3 96.6 - - + +
108A PRO* 1.3 64.0 - - - +
109A GLN* 3.3 3.1 - - - -
110A ALA* 3.3 10.3 + - + +
111A SER* 3.0 20.6 + - - -
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Residues in contact with PRO 108 (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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104A SER 3.5 16.1 - - - +
105A ARG 3.6 11.7 - - - +
106A ASP 3.3 8.3 - - - +
107A TYR* 1.3 91.4 - - - +
109A GLN* 1.3 59.7 + - + +
111A SER* 3.2 3.2 + - - -
112A ARG* 2.9 54.8 + - - +
173A ALA* 4.0 18.7 - - + +
188A ARG* 6.1 3.8 - - - +
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Residues in contact with GLN 109 (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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27A LEU* 3.8 27.0 - - + +
28A ASP* 2.6 36.0 + - - +
31A SER* 3.3 24.5 + - - +
107A TYR 3.3 0.4 - - - -
108A PRO* 1.3 79.1 - - + +
110A ALA* 1.3 65.8 + - - +
112A ARG* 3.2 18.1 + - + +
113A LEU* 3.1 18.5 + - - +
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Residues in contact with ALA 110 (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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27A LEU* 3.9 23.2 - - + +
68A VAL* 5.9 2.2 - - + +
69A LEU* 5.1 0.5 - - - +
72A ILE* 3.6 35.1 - - + +
107A TYR* 3.3 18.7 + - + +
109A GLN* 1.3 79.9 - - - +
111A SER* 1.3 64.0 + - - +
113A LEU* 3.3 3.7 + - - +
114A PHE* 3.2 20.6 + - - +
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Residues in contact with SER 111 (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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72A ILE* 4.4 1.1 - - - +
76A TRP* 3.7 31.6 - - - -
103A VAL* 5.7 0.4 - - - -
104A SER* 4.9 4.0 + - - -
107A TYR 3.0 14.4 + - - -
108A PRO* 3.4 9.6 - - - -
110A ALA* 1.3 76.8 - - - +
112A ARG* 1.3 62.5 + - - +
114A PHE* 3.1 4.7 + - - +
115A CYS* 3.1 21.8 + - - +
170A GLN* 4.1 7.3 - - - +
173A ALA* 4.0 12.3 - - - +
174A ASP* 2.7 26.7 + - - +
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Residues in contact with ARG 112 (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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31A SER* 5.8 1.8 - - - -
108A PRO* 2.9 43.9 + - - +
109A GLN* 3.2 17.4 + - + +
111A SER* 1.3 76.6 - - - +
113A LEU* 1.3 57.7 + - - +
115A CYS* 3.3 6.1 + - - +
116A MSE 2.9 40.3 + - + +
173A ALA 3.1 25.1 + - - +
174A ASP* 4.0 13.7 + - - +
176A ALA* 3.7 15.4 - - - +
177A PRO* 5.1 3.6 - - - +
118B MSE 5.1 2.4 + - - -
119B LEU* 3.6 39.9 + - + +
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Residues in contact with LEU 113 (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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27A LEU* 4.1 13.2 - - + -
30A PHE* 3.7 24.0 - - + +
31A SER* 3.5 35.8 - - - +
34A GLY* 5.9 0.7 - - - -
65A TYR* 4.4 15.7 - - + +
68A VAL* 3.5 31.9 - - + -
69A LEU* 3.8 12.6 - - + -
109A GLN 3.1 15.3 + - - +
110A ALA 3.8 4.7 - - - +
111A SER 3.3 0.2 - - - -
112A ARG* 1.3 73.2 - - - +
114A PHE* 1.3 67.0 + - - +
116A MSE 3.1 14.4 + - + +
117A GLU* 3.0 22.9 + - - +
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Residues in contact with PHE 114 (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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69A LEU* 3.5 19.6 - - + +
72A ILE* 4.5 10.3 - - + -
73A LEU* 3.9 19.3 - - + -
76A TRP* 3.4 34.8 - + + -
110A ALA 3.2 10.2 + - - +
111A SER 3.1 9.5 + - - +
113A LEU* 1.3 76.7 - - - +
115A CYS* 1.3 66.0 + - - +
117A GLU* 3.2 4.5 + - - +
118A MSE 3.1 47.2 + - + +
125A LEU* 3.6 26.9 - - + -
129A LEU* 4.3 2.7 - - + -
212A URA 3.7 12.8 - - - -
175B PHE* 4.0 6.3 - + - -
178B GLN* 3.4 26.7 - - - -
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Residues in contact with CYS 115 (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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111A SER 3.1 5.1 + - - +
112A ARG 3.4 9.2 - - - +
114A PHE* 1.3 81.5 - - - +
116A MSE 1.3 62.0 + - - +
118A MSE 3.0 5.8 + - - +
119A LEU* 3.0 26.6 + - - +
174A ASP* 3.4 29.8 - - - +
175A PHE* 5.9 0.2 - - - -
115B CYS* 3.9 27.4 - - - -
119B LEU* 3.9 10.1 - - + -
175B PHE* 3.8 29.1 - - + -
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Residues in contact with MSE 116 (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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30A PHE 4.7 2.2 - - - +
31A SER* 3.1 46.2 - - - +
34A GLY* 5.8 3.8 - - - -
65A TYR* 5.7 0.7 - - - +
112A ARG* 2.9 28.8 + - + +
113A LEU* 3.1 18.1 + - + +
115A CYS* 1.3 71.8 - - - +
117A GLU* 1.3 64.1 + - - +
119A LEU* 3.0 10.1 + - + +
120A ALA* 2.9 22.2 + - - +
119B LEU* 3.3 48.0 - - + +
120B ALA* 4.8 3.6 - - + +
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Residues in contact with GLU 117 (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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35A PHE* 5.6 0.2 - - - +
65A TYR* 2.5 46.3 + - - +
69A LEU* 3.9 13.5 - - + -
113A LEU 3.0 9.9 + - - +
114A PHE 3.5 8.5 - - - +
116A MSE 1.3 76.8 - - - +
118A MSE 1.3 69.9 + - + +
120A ALA* 3.1 12.3 + - - +
121A GLY 3.5 0.2 + - - -
122A ALA* 2.8 39.5 + - - -
123A PRO* 3.3 7.1 - - - +
124A LEU* 2.8 34.1 + - - +
125A LEU* 3.0 19.3 + - + -
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Residues in contact with MSE 118 (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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114A PHE* 3.1 43.3 + - + +
115A CYS* 3.0 9.2 + - - +
117A GLU* 1.3 84.2 - - + +
119A LEU* 1.3 66.1 + - - +
121A GLY 2.9 12.3 + - - -
122A ALA* 3.9 14.1 - - + +
125A LEU* 3.8 20.6 - - + -
129A LEU* 4.1 9.6 - - + -
112B ARG* 5.4 1.4 - - - -
174B ASP 3.5 18.6 - - - +
175B PHE* 3.6 30.5 - - + -
177B PRO* 3.4 16.8 - - + +
178B GLN* 3.8 29.8 - - - -
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Residues in contact with LEU 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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115A CYS* 3.0 17.0 + - - +
116A MSE 3.0 9.7 + - + +
118A MSE 1.3 76.6 - - - +
120A ALA* 1.3 61.3 + - - +
121A GLY 3.1 1.6 + - - -
112B ARG* 3.9 32.0 + - + +
115B CYS* 3.8 13.9 - - + -
116B MSE 3.7 51.5 - - + +
119B LEU* 3.7 28.5 - - + -
174B ASP* 3.6 39.7 - - + +
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Residues in contact with ALA 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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116A MSE 2.9 11.9 + - - +
117A GLU* 3.6 15.3 - - - +
118A MSE 3.0 1.2 - - - -
119A LEU* 1.3 77.1 - - - +
121A GLY* 1.3 57.9 + - - +
123A PRO* 3.4 22.5 - - + +
116B MSE 5.8 0.9 - - - -
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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