Contacts of the helix formed by residues 126 - 139 (chain A) in PDB entry 5FOR
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 GLU 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ASP 3.9 6.1 + - - +
125A ASP* 1.3 77.7 + - - +
127A PRO* 1.3 66.5 - - - +
128A GLU* 3.1 28.7 - - + +
129A THR* 2.8 38.7 + - - +
130A TYR* 3.3 5.6 + - - -
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Residues in contact with PRO 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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23A TYR* 3.8 20.9 - - - +
27A LEU* 4.0 16.7 - - + +
125A ASP 3.6 4.4 - - - +
126A GLU* 1.3 94.7 - - + +
128A GLU* 1.3 70.9 + - - +
130A TYR* 3.1 27.2 + - + +
131A VAL* 3.2 16.8 + - - +
1140A 1PE 5.6 1.1 - - - +
1141A I3C 4.0 8.7 - - + +
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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
----------------------------------------------------------
126A GLU* 3.6 29.5 - - + +
127A PRO* 1.3 86.8 - - - +
129A THR* 1.3 59.7 + - - +
131A VAL* 3.1 11.5 - - - +
132A ALA* 3.0 30.8 + - - +
1141A I3C 4.0 17.9 - - + +
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Residues in contact with THR 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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121A LEU* 3.8 20.6 - - + -
125A ASP* 3.9 21.2 + - - +
126A GLU* 2.8 26.3 + - - +
128A GLU* 1.3 78.2 - - - +
130A TYR* 1.3 61.8 + - - -
132A ALA* 3.5 5.4 + - - +
133A ALA* 3.1 22.7 + - - +
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Residues in contact with TYR 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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20A TRP* 3.7 15.1 - + - -
23A TYR* 4.0 22.4 - + - -
24A LEU* 4.3 13.2 - - + -
27A LEU* 3.9 19.5 - - + -
28A PHE* 4.2 4.4 - - + -
98A LEU* 4.1 5.6 - - + -
121A LEU* 3.5 33.5 - - + +
122A THR 2.5 30.8 + - - -
123A CYS 3.6 10.6 + - - -
125A ASP* 3.5 35.4 + - + -
126A GLU 3.3 0.4 + - - -
127A PRO* 3.1 23.7 + - + +
129A THR* 1.3 77.5 - - - +
131A VAL* 1.3 61.5 + - - +
133A ALA* 3.3 6.1 + - - +
134A VAL* 3.3 24.6 + - - +
1140A 1PE 5.1 2.5 - - - -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.9 20.6 - - + -
28A PHE* 4.2 13.9 - - + -
31A SER* 3.9 19.3 - - - +
33A GLN* 4.3 3.4 - - + +
34A VAL* 4.7 3.8 - - + +
127A PRO 3.2 3.3 + - - +
128A GLU 3.1 13.5 - - - +
130A TYR* 1.3 71.0 - - - +
132A ALA* 1.3 59.3 + - + +
133A ALA 3.1 1.6 - - - -
134A VAL* 3.3 6.2 + - + +
135A LYS* 2.7 37.3 + - - +
1141A I3C 3.3 58.1 - - + +
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Residues in contact with ALA 132 (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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33A GLN* 5.7 2.7 - - - +
128A GLU 3.0 20.3 + - - +
129A THR* 3.9 5.8 - - - +
131A VAL* 1.3 76.8 - - + +
133A ALA* 1.3 57.4 + - - +
135A LYS* 3.4 7.0 + - - +
136A MLY 2.9 30.1 + - - +
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Residues in contact with ALA 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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96A VAL* 4.3 5.2 - - + -
119A GLN* 2.8 44.1 - - + +
121A LEU* 4.1 20.6 - - + -
129A THR* 3.1 14.4 + - + +
130A TYR 3.5 8.5 - - - +
131A VAL 3.1 0.2 - - - -
132A ALA* 1.3 77.7 - - - +
134A VAL* 1.3 58.3 + - - +
136A MLY 3.2 1.0 + - - -
137A ALA* 3.0 23.7 + - - +
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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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9A ILE* 3.9 16.6 - - + -
28A PHE* 3.4 38.8 - - + -
34A VAL* 3.5 24.5 - - + -
63A CYS* 4.6 5.4 - - - -
65A VAL* 3.9 21.3 - - + -
96A VAL* 4.9 6.7 - - + -
121A LEU* 5.9 0.7 - - + -
130A TYR 3.3 7.1 + - - +
131A VAL* 3.3 7.5 + - - +
133A ALA* 1.3 75.7 - - + +
135A LYS* 1.3 68.1 + - - +
137A ALA* 4.1 6.7 - - - -
138A ILE* 3.2 28.8 + - - +
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Residues in contact with LYS 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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33A GLN* 3.4 53.6 + - + +
34A VAL* 4.4 1.1 - - + -
37A GLN* 5.1 4.9 - - - +
131A VAL 2.7 22.4 + - - +
132A ALA* 3.6 9.0 - - - +
134A VAL* 1.3 78.1 - - - +
136A MLY 1.3 62.7 + - - +
138A ILE* 3.5 15.8 + - + +
139A SER* 3.3 31.5 + - - -
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Residues in contact with MLY 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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93A HIS 5.1 2.4 - - - +
94A ARG* 4.9 0.5 + - - -
119A GLN* 3.3 31.4 - - - +
132A ALA 2.9 18.1 + - - +
133A ALA 3.7 2.9 - - - +
135A LYS* 1.3 76.6 + - - +
137A ALA* 1.3 63.4 + - - +
139A SER* 3.1 24.2 + - - +
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Residues in contact with ALA 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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63A CYS* 3.7 27.4 - - + +
93A HIS 3.8 19.2 - - - +
94A ARG* 2.7 41.5 + - - +
96A VAL* 4.1 13.7 - - + -
119A GLN* 4.8 2.0 - - - +
133A ALA 3.0 16.2 + - - +
134A VAL 3.9 1.6 - - - +
135A LYS 3.2 0.4 - - - -
136A MLY 1.3 79.3 + - - +
138A ILE* 1.3 52.7 + - - +
139A SER 3.3 0.2 - - - -
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Residues in contact with ILE 138 (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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8A ASP 4.0 7.0 - - - +
9A ILE* 3.9 17.0 - - + -
33A GLN 4.5 0.2 - - - +
34A VAL* 4.2 16.8 - - + -
37A GLN* 3.7 39.0 - - + +
62A ARG* 2.8 36.7 + - + +
63A CYS* 3.5 26.0 - - + -
94A ARG* 3.5 2.9 - - - +
134A VAL 3.2 18.2 + - - +
135A LYS* 3.5 22.2 - - + +
137A ALA* 1.3 74.4 - - - +
139A SER* 1.3 60.9 + - - +
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Residues in contact with SER 139 (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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62A ARG* 3.5 8.2 + - - -
94A ARG* 2.9 25.8 + - - -
135A LYS* 3.3 27.4 + - - -
136A MLY 3.1 20.5 + - - +
137A ALA 3.3 2.0 - - - -
138A ILE* 1.3 78.9 - - - +
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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