Contacts of the helix formed by residues 123 - 142 (chain A) in PDB entry 2FYU
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 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A SER* 3.8 30.3 + - - +
122A LEU* 1.3 73.8 - - - +
124A ASP* 1.3 59.4 + - - +
125A SER* 3.3 12.1 - - - +
126A GLN* 2.9 37.0 + - + +
127A ILE* 3.1 11.1 + - - +
179A ARG* 4.5 4.6 + - - +
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Residues in contact with ASP 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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122A LEU 3.5 0.8 + - - +
123A GLU* 1.3 73.2 + - - +
125A SER* 1.3 59.7 + - - +
127A ILE* 3.5 21.8 - - + +
128A GLU* 3.2 22.9 + - - +
179A ARG* 3.9 34.2 + - - +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 4.3 9.7 - - - +
124A ASP* 1.3 74.7 - - - +
126A GLN* 1.3 62.1 + - - +
128A GLU* 3.7 6.7 + - - +
129A LYS* 3.2 36.1 + - - +
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Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.8 13.2 - - + +
65A LYS* 3.8 42.9 - - + +
123A GLU* 2.9 24.1 + - + +
125A SER* 1.3 79.6 + - - +
127A ILE* 1.4 58.0 + - - +
129A LYS* 3.1 25.2 + - - +
130A GLU* 3.0 60.3 + - - +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.4 28.4 - - + -
62A LEU* 3.6 18.5 - - + +
122A LEU* 4.0 16.2 - - + +
123A GLU 3.1 17.2 + - - +
124A ASP* 3.5 26.2 + - + +
126A GLN* 1.4 72.3 - - - +
128A GLU* 1.3 80.1 + - - +
130A GLU 3.4 0.7 + - - -
131A ARG* 3.0 42.4 + - - +
177A LEU 4.5 5.8 - - - +
178A SER* 5.5 1.1 - - - -
179A ARG* 4.6 20.2 - - + +
182A LEU* 4.9 6.1 - - + -
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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 ASP 3.2 14.5 + - - +
125A SER* 3.8 8.7 - - - +
126A GLN 3.3 0.4 - - - -
127A ILE* 1.3 86.0 - - - +
129A LYS* 1.3 63.8 + - - +
131A ARG* 2.9 54.4 + - - +
132A ASP* 3.9 11.1 + - - +
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Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A SER* 3.2 21.8 + - - +
126A GLN* 3.1 26.4 + - - +
128A GLU* 1.3 73.2 - - - +
130A GLU* 1.3 69.4 - - - +
132A ASP* 3.4 17.8 + - - +
133A VAL* 3.4 16.7 + - + +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 4.0 12.1 - - + -
61A HIS* 3.1 56.0 + - + +
62A LEU* 3.8 14.1 - - + -
65A LYS* 3.4 15.7 + - - -
126A GLN* 3.0 37.0 + - - +
127A ILE 3.7 4.7 - - - +
128A GLU 3.3 0.2 - - - -
129A LYS* 1.3 78.6 - - - +
131A ARG* 1.3 56.9 + - - +
133A VAL* 3.7 14.7 - - - +
134A ILE* 2.9 40.4 + - + +
287B ARG* 5.3 1.7 - - - +
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Residues in contact with ARG 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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58A PHE* 3.9 9.9 - - + -
127A ILE* 3.0 34.2 + - - +
128A GLU* 2.9 58.6 + - - +
130A GLU* 1.3 73.6 - - - +
132A ASP* 1.3 60.1 + - - +
134A ILE 3.5 0.3 + - - -
135A LEU* 3.1 37.4 + - + +
174A VAL* 3.4 27.5 + - + +
175A ARG* 2.9 37.7 + - + +
176A LYS* 4.3 1.2 - - - +
177A LEU 2.6 33.1 + - - +
178A SER* 4.9 0.8 - - - +
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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
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128A GLU 4.1 10.2 - - - +
129A LYS* 3.4 10.6 + - - +
130A GLU 3.3 0.4 - - - -
131A ARG* 1.3 77.2 - - - +
133A VAL* 1.3 64.1 + - + +
135A LEU* 3.7 15.9 + - - +
136A GLN* 3.2 30.8 + - + +
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Residues in contact with VAL 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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61A HIS* 3.6 21.5 - - + +
129A LYS* 3.4 15.7 + - + +
130A GLU* 3.2 22.9 + - - +
132A ASP* 1.3 73.6 - - + +
134A ILE* 1.3 63.0 + - - +
136A GLN* 3.3 8.9 + - - +
137A GLU* 3.1 34.6 + - + +
287B ARG* 4.6 5.4 - - - -
34I VAL 4.4 18.8 - - - +
36I ALA* 5.1 5.6 - - + +
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Residues in contact with ILE 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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57A TYR* 3.7 21.1 - - + -
58A PHE* 3.6 54.3 - - + +
61A HIS* 3.5 29.8 - - + +
130A GLU 2.9 25.9 + - - +
133A VAL* 1.3 70.3 - - - +
135A LEU* 1.3 56.6 + - - +
137A GLU* 3.1 10.8 + - - +
138A LEU* 2.9 31.6 + - + +
168A GLU 4.7 2.9 - - - +
174A VAL* 3.7 30.1 - - + -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 3.1 27.5 + - + +
132A ASP* 3.9 19.1 - - - +
133A VAL 3.4 0.2 - - - -
134A ILE* 1.3 74.7 - - - +
136A GLN* 1.3 59.2 + - + +
138A LEU* 3.2 11.5 + - + +
139A GLN* 3.1 28.6 + - - +
171A SER* 3.9 33.9 - - - +
174A VAL* 3.8 19.7 - - + -
175A ARG* 3.7 30.5 - - + +
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASP* 3.2 18.0 + - + +
133A VAL* 3.3 8.3 + - - +
135A LEU* 1.3 74.1 - - + +
137A GLU* 1.3 60.5 + - - +
139A GLN* 3.3 27.4 + - - +
140A GLU* 2.9 33.1 + - - +
36I ALA* 3.8 21.1 - - + -
37I THR* 2.8 37.5 + - - +
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Residues in contact with GLU 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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57A TYR* 2.6 33.4 + - + +
61A HIS* 2.8 27.7 + - - -
133A VAL* 3.1 21.4 + - + +
134A ILE* 3.3 7.8 - - - +
136A GLN* 1.3 73.9 - - - +
138A LEU* 1.3 52.8 + - + +
140A GLU* 3.4 20.0 - - - +
141A ASN* 2.8 47.4 + - - +
287B ARG* 2.8 30.5 + - - -
33I ALA 5.5 3.9 - - - +
34I VAL* 6.1 1.0 - - - -
36I ALA* 5.4 3.6 - - + -
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Residues in contact with LEU 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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57A TYR* 5.8 0.2 - - + -
134A ILE* 2.9 20.0 + - + +
135A LEU* 3.2 14.1 + - + +
137A GLU* 1.3 73.5 - - + +
139A GLN* 1.3 58.5 + - - +
141A ASN* 3.4 10.5 + - + +
142A ASP* 3.1 37.5 + - - +
168A GLU* 3.7 33.7 - - + +
169A GLY 4.1 10.5 - - - +
171A SER* 4.1 25.4 - - - +
174A VAL* 4.1 24.0 - - + -
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Residues in contact with GLN 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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135A LEU* 3.1 13.0 + - - +
136A GLN* 3.3 30.9 + - - +
138A LEU* 1.3 73.1 - - - +
140A GLU* 1.3 61.7 + - - +
142A ASP* 3.4 19.8 - - - +
143A THR* 3.8 11.6 - - - +
37I THR* 4.1 18.6 - - + +
39I GLU* 4.5 14.7 + - - +
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Residues in contact with GLU 140 (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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136A GLN 2.9 17.4 + - - +
137A GLU* 3.4 24.6 - - - +
138A LEU 3.3 0.2 - - - -
139A GLN* 1.3 73.5 - - - +
141A ASN* 1.4 63.2 + - - +
143A THR* 2.7 32.4 + - - -
144A SER* 3.9 2.8 + - - -
33I ALA* 3.9 15.3 - - - +
36I ALA* 3.3 13.1 - - - +
37I THR* 2.8 37.2 + - + -
38I SER* 3.6 25.2 + - - +
39I GLU* 4.7 4.9 - - - +
40I SER* 5.6 0.3 + - - -
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Residues in contact with ASN 141 (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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57A TYR* 5.0 4.1 + - - -
137A GLU* 2.8 35.9 + - - +
138A LEU* 3.4 12.1 + - + +
140A GLU* 1.4 77.0 + - - +
142A ASP* 1.3 57.8 + - - +
144A SER* 3.0 36.3 + - - +
147A ASP* 4.4 17.4 + - + +
148A VAL* 3.7 5.9 - - - +
151A ASN* 6.1 3.1 - - - +
168A GLU* 3.6 29.9 - - - +
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Residues in contact with ASP 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.1 18.8 + - - +
139A GLN* 3.4 17.6 - - - +
141A ASN* 1.3 75.8 - - - +
143A THR* 1.3 59.1 + - + +
144A SER 3.3 0.6 + - - -
148A VAL* 3.7 20.1 - - - +
425A PHE* 4.6 11.8 - - - -
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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
------------------------------------------------------------
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