Contacts of the helix formed by residues 125 - 137 (chain A) in PDB entry 5F0L
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 SER 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TYR 3.9 0.3 + - - -
122A PHE* 3.0 17.1 + - - +
124A GLN* 1.3 79.5 - - - +
126A ARG* 1.3 62.9 + - - +
127A LYS 3.5 2.0 - - - -
128A ASP* 3.7 10.5 + - - +
129A ILE* 3.1 46.6 + - - +
173A THR* 4.0 0.2 - - - -
4C THR* 6.2 0.9 - - - -
5C VAL* 3.4 31.2 - - - +
6C ALA* 5.6 1.6 - - - -
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 3.4 32.1 - - + -
122A PHE 4.0 0.6 + - - -
123A PRO* 3.2 18.0 + - + +
125A SER* 1.3 77.5 - - - +
127A LYS* 1.3 64.0 + - - +
129A ILE* 4.0 0.5 - - - +
130A LEU* 3.0 42.3 + - + +
160A ILE 3.4 23.4 + - - -
162A PRO* 3.7 16.6 - - - +
166A GLU* 3.2 40.2 + - - -
172A THR* 4.6 17.8 + - - +
173A THR* 2.9 20.5 + - - +
174A GLY 2.9 26.1 + - - -
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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
----------------------------------------------------------
126A ARG* 1.3 78.9 - - - +
128A ASP* 1.3 68.0 + - - +
130A LEU* 4.0 4.8 - - - +
131A LYS* 3.0 34.9 + - + +
173A THR* 3.1 20.2 + - - +
174A GLY* 3.8 17.3 - - - +
178A ASP* 3.7 39.4 + - + +
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN 5.8 0.9 - - - -
125A SER* 3.7 13.5 + - - +
126A ARG 3.3 0.2 - - - -
127A LYS* 1.3 89.3 - - - +
129A ILE* 1.3 53.3 + - + +
131A LYS* 3.5 5.7 + - - +
132A ASP* 2.8 35.7 + - - +
173A THR* 6.0 0.2 - - - -
8C THR* 4.0 23.5 + - + +
10C ARG* 4.8 1.2 + - - -
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Residues in contact with ILE 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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95A TYR* 4.2 14.4 - - + +
115A GLY* 3.8 12.3 - - - +
118A TYR* 3.6 31.2 - - + -
119A VAL* 3.8 22.2 - - + -
125A SER* 3.1 44.4 + - - +
128A ASP* 1.3 73.6 - - + +
130A LEU* 1.3 60.7 + - - +
132A ASP* 3.2 6.7 + - - +
133A LEU* 2.8 49.2 + - + +
6C ALA* 4.5 11.7 - - + -
8C THR* 4.6 3.8 - - + -
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 6.0 0.2 - - + -
119A VAL* 4.6 5.6 - - + -
126A ARG* 3.0 42.1 + - + +
127A LYS* 4.0 4.5 - - - +
129A ILE* 1.3 72.5 - - - +
131A LYS* 1.3 67.9 + - - +
133A LEU* 3.2 6.9 + - + -
134A VAL* 3.2 19.8 + - - +
157A THR* 3.7 31.0 - - + -
160A ILE* 4.5 15.5 - - + +
161A LEU* 3.9 16.6 - - + -
162A PRO* 3.6 25.1 - - + -
178A ASP* 6.4 1.3 - - + -
182A PHE* 3.4 25.5 - - + -
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Residues in contact with LYS 131 (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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127A LYS* 3.0 23.8 + - + +
128A ASP* 3.7 5.8 - - - +
130A LEU* 1.3 76.1 - - - +
132A ASP* 1.3 61.7 + - - +
134A VAL* 3.3 15.2 - - + +
135A GLU* 3.1 60.3 + - - +
181A ASP* 5.6 9.8 + - + +
182A PHE* 5.2 2.1 - - - +
185A LEU* 3.6 18.2 - - - +
10C ARG* 3.7 16.4 - - - +
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 2.5 31.4 + - - +
111A LEU* 4.8 2.1 - - - +
128A ASP 2.8 21.7 + - - +
129A ILE 3.3 5.8 - - - +
130A LEU 3.1 0.2 - - - -
131A LYS* 1.3 70.7 - - - +
133A LEU* 1.3 61.0 + - - +
135A GLU* 3.1 2.1 + - - +
136A MET* 2.9 42.7 + - - +
249B ARG* 2.5 37.4 + - - -
8C THR* 3.8 12.2 - - + +
10C ARG* 3.1 20.7 + - - +
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Residues in contact with LEU 133 (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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95A TYR* 3.9 8.1 - - - +
111A LEU* 3.6 42.0 - - + +
112A ILE* 3.8 22.8 - - + +
115A GLY* 4.1 12.6 - - - -
116A VAL* 4.7 2.0 - - + +
119A VAL* 5.8 0.2 - - + -
129A ILE* 2.8 41.4 + - + +
130A LEU* 3.2 8.7 + - + +
132A ASP* 1.3 73.8 - - - +
134A VAL* 1.3 61.3 + - - +
136A MET* 4.3 3.6 - - - +
137A CYS* 3.3 28.1 + - - -
153A LEU* 3.7 22.2 - - + -
157A THR* 5.0 9.4 - - + -
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Residues in contact with VAL 134 (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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130A LEU 3.2 10.2 + - - +
131A LYS* 3.3 22.0 - - - +
133A LEU* 1.3 77.9 - - - +
135A GLU* 1.3 65.1 + - - +
137A CYS* 3.6 2.4 + - - +
150A ARG* 3.4 37.0 + - - +
153A LEU* 3.7 16.2 - - + +
182A PHE* 3.7 41.5 - - + +
185A LEU* 3.8 29.6 - - + +
186A ASN* 4.0 7.0 - - + +
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Residues in contact with GLU 135 (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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131A LYS* 3.1 46.6 + - - +
132A ASP 3.1 3.4 + - - +
134A VAL* 1.3 79.7 - - + +
136A MET* 1.3 62.2 + - - +
138A ARG* 2.6 69.2 + - - +
185A LEU* 3.3 15.6 - - - +
247B PRO* 4.0 1.0 - - - +
10C ARG* 3.3 35.9 + - - +
13C THR* 4.4 5.8 + - - -
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Residues in contact with MET 136 (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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99A GLN* 4.7 3.1 - - - +
104A ILE* 5.2 0.9 - - - +
108A LEU* 3.7 30.9 - - + +
111A LEU* 4.4 9.0 - - + -
132A ASP* 2.9 36.5 + - - +
133A LEU 4.5 2.5 - - - +
134A VAL 3.5 0.2 - - - -
135A GLU* 1.3 69.6 - - - +
137A CYS* 1.3 62.1 + - - +
138A ARG 3.2 0.7 - - - -
139A GLY* 3.3 12.0 + - - -
247B PRO* 3.9 28.3 - - + +
248B ILE 4.9 0.2 - - - -
249B ARG* 3.6 55.9 - - + +
10C ARG* 3.6 18.8 - - - -
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Residues in contact with CYS 137 (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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108A LEU* 4.3 11.2 - - - -
112A ILE* 3.9 17.7 - - - -
133A LEU 3.3 20.0 + - - -
134A VAL 3.7 4.3 - - - +
135A GLU 3.2 0.8 - - - -
136A MET* 1.3 73.1 - - - +
138A ARG* 1.3 60.4 + - - +
139A GLY 2.9 7.4 + - - -
140A VAL* 3.1 22.1 + - - +
149A LEU* 3.9 25.9 - - + +
150A ARG* 3.5 35.0 + - + +
153A LEU* 4.4 11.4 - - - -
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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