Contacts of the helix formed by residues 112 - 129 (chain A) in PDB entry 3FEG
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 GLY 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLN* 1.3 79.0 - - - +
113A VAL* 1.3 65.9 + - - -
114A ASP 3.3 2.7 - - - -
115A SER* 3.2 10.6 + - - -
116A LEU* 2.9 20.6 + - - +
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Residues in contact with VAL 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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111A GLN 3.7 1.2 + - - -
112A GLY* 1.3 69.8 - - - -
114A ASP* 1.3 69.2 + - - +
116A LEU* 3.0 8.2 + - - +
117A VAL* 2.9 41.7 + - + +
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Residues in contact with ASP 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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112A GLY* 4.5 0.2 - - - -
113A VAL* 1.3 90.7 - - - +
115A SER* 1.3 63.3 + - - +
117A VAL* 3.3 9.2 + - - +
118A LEU* 3.0 33.8 + - + +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 2.9 25.6 + - - +
112A GLY* 3.2 16.4 + - - -
113A VAL 3.2 0.4 - - - -
114A ASP* 1.3 79.8 - - - +
116A LEU* 1.3 57.2 + - - +
118A LEU* 3.3 9.6 + - - +
119A GLU* 2.9 29.5 + - - +
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Residues in contact with LEU 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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106A TYR* 4.0 36.6 - - + +
111A GLN* 3.9 29.4 - - + +
112A GLY 2.9 14.4 + - - +
113A VAL* 3.0 9.2 + - - +
115A SER* 1.3 73.3 - - - +
117A VAL* 1.3 65.4 + - - +
119A GLU* 4.3 9.2 - - - -
120A SER* 2.9 44.3 + - - +
139A PHE 6.0 0.4 - - - +
140A PRO* 5.2 5.4 - - + +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 2.9 28.6 + - + +
114A ASP* 3.6 10.3 - - - +
116A LEU* 1.3 78.1 - - + +
118A LEU* 1.3 71.2 + - + +
120A SER* 3.9 2.9 - - - -
121A VAL* 2.9 42.3 + - + +
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Residues in contact with LEU 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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2A UNX 4.1 17.3 - - - -
114A ASP* 3.0 25.7 + - + +
115A SER* 3.7 6.7 - - - +
117A VAL* 1.3 84.4 - - + +
119A GLU* 1.3 57.8 + - - +
121A VAL* 4.6 0.7 - - + -
122A MET* 2.9 36.3 + - + +
180A PRO 5.3 1.1 - - - +
181A PHE* 3.7 32.1 - - + -
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Residues in contact with GLU 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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104A ARG* 5.7 1.0 - - - -
106A TYR* 3.8 19.2 + - - -
111A GLN* 2.8 27.9 + - - +
115A SER 2.9 16.6 + - - +
116A LEU* 3.8 10.4 - - - +
117A VAL 3.3 0.2 - - - -
118A LEU* 1.3 77.9 - - - +
120A SER* 1.3 58.4 + - - +
122A MET* 3.5 10.4 + - - +
123A PHE* 3.0 26.4 + - + +
143A ARG* 3.4 24.1 + - - +
265A PHE 6.1 1.3 - - - +
266A GLU* 6.1 3.1 - - - -
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Residues in contact with SER 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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106A TYR* 4.2 9.2 + - - -
116A LEU* 2.9 33.2 + - - +
117A VAL* 3.9 3.4 - - - -
119A GLU* 1.3 76.6 - - - +
121A VAL* 1.3 67.7 + - - +
123A PHE* 3.4 5.5 + - - +
124A ALA* 3.0 25.6 + - - +
135A LEU* 4.6 4.0 - - - +
138A VAL* 5.0 16.6 - - - +
143A ARG* 5.5 2.2 - - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 2.9 33.9 + - + +
118A LEU* 3.9 4.3 - - + +
120A SER* 1.3 75.8 - - - +
122A MET* 1.3 64.7 + - - +
124A ALA* 3.3 6.2 + - - +
125A ILE* 2.9 44.1 + - + +
180A PRO* 4.1 15.5 - - + -
181A PHE* 4.2 7.4 - - + -
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Residues in contact with MET 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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118A LEU* 2.9 21.9 + - + +
119A GLU* 3.6 8.5 - - - +
121A VAL* 1.3 80.0 - - - +
123A PHE* 1.3 62.3 + - - +
125A ILE* 3.3 1.2 + - - +
126A LEU* 3.0 37.7 + - + +
179A MET* 4.0 14.8 - - + -
181A PHE* 3.7 24.9 - - + -
238A PHE* 3.8 14.8 - - + -
265A PHE* 3.8 24.2 - - - +
268A SER* 3.5 42.6 - - - +
269A SER* 5.3 0.2 - - - -
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Residues in contact with PHE 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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104A ARG* 5.8 0.2 - - - -
119A GLU* 3.0 17.2 + - + +
120A SER* 3.8 5.6 - - - +
122A MET* 1.3 77.6 - - - +
124A ALA* 1.3 62.8 + - - +
126A LEU* 3.5 5.1 + - - +
127A ALA* 3.0 19.9 + - - +
132A GLY* 5.9 0.2 - - - -
133A PRO* 3.4 36.1 - - + +
134A GLN 4.0 5.8 - - - -
135A LEU* 3.9 25.8 - - + -
143A ARG* 3.3 35.4 - - - +
145A GLU* 3.5 35.9 - - + -
264A ASP 6.3 0.4 - - - -
265A PHE* 3.9 32.2 - + + +
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Residues in contact with ALA 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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120A SER 3.0 18.8 + - - +
121A VAL* 3.7 6.7 - - - +
122A MET 3.2 0.2 - - - -
123A PHE* 1.3 78.6 - - - +
125A ILE* 1.3 63.1 + - + +
127A ALA* 3.4 6.3 + - - +
128A GLU* 3.1 28.1 + - + +
135A LEU* 3.8 24.0 - - + -
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Residues in contact with ILE 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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121A VAL* 2.9 33.2 + - + +
122A MET 3.9 3.1 - - - +
124A ALA* 1.3 76.5 - - + +
126A LEU* 1.3 65.7 + - - +
128A GLU* 3.1 9.3 + - + +
129A ARG* 3.0 58.6 + - - +
179A MET* 3.7 16.6 - - + -
180A PRO* 3.5 33.0 - - + -
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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 MET* 3.0 33.2 + - + +
123A PHE 4.0 3.4 - - - +
125A ILE* 1.3 75.0 - - + +
127A ALA* 1.3 61.0 + - - +
129A ARG* 3.2 3.1 + - - -
130A SER 3.0 3.6 + - - -
131A LEU* 2.8 45.1 + - + -
132A GLY* 3.8 12.8 - - - +
174A PHE* 4.0 20.0 - - + -
177A MET* 4.4 18.8 - - + -
179A MET* 4.1 17.3 - - + -
238A PHE* 4.4 2.7 - - + -
265A PHE* 3.6 45.1 - - + -
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Residues in contact with ALA 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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123A PHE 3.0 12.5 + - - +
124A ALA* 3.4 12.8 - - - +
125A ILE 3.1 0.2 - - - -
126A LEU* 1.3 77.4 - - - +
128A GLU* 1.3 65.3 + - - +
130A SER* 3.1 10.0 + - - -
132A GLY* 3.7 11.8 - - - +
133A PRO 3.3 22.2 - - - +
134A GLN* 2.8 38.7 + - - +
135A LEU* 4.1 7.4 - - + +
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Residues in contact with GLU 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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124A ALA* 3.1 16.4 + - + +
125A ILE* 3.1 11.1 + - + +
127A ALA* 1.3 78.6 - - - +
129A ARG* 1.3 63.4 + - + +
130A SER* 3.5 5.9 + - - -
134A GLN* 4.6 9.5 - - - +
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Residues in contact with ARG 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 ILE* 3.0 37.9 + - - +
126A LEU* 3.9 4.7 - - - +
127A ALA 3.1 0.4 - - - -
128A GLU* 1.3 79.5 - - + +
130A SER* 1.3 72.1 + - - +
131A LEU* 3.2 10.2 + - + +
177A MET* 3.5 40.6 - - + +
178A GLU* 2.8 35.7 + - - +
179A MET* 3.7 6.5 - - - -
180A PRO* 5.9 0.4 - - - +
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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