Contacts of the helix formed by residues 140 - 155 (chain A) in PDB entry 2F4N
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ARG* 1.3 69.1 + - - +
142A ASP 3.2 2.9 - - - -
143A VAL* 2.9 36.6 + - - +
144A TYR* 3.7 17.7 + - - -
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Residues in contact with ARG 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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21A PHE* 3.9 18.4 - - + -
27A TYR* 6.0 2.7 - - + -
31A MSE 3.1 36.0 - - + +
82A VAL* 5.0 4.3 - - + -
140A GLY* 1.3 71.9 - - - +
142A ASP* 1.3 60.4 + - - +
143A VAL 3.0 5.5 + - - -
144A TYR* 3.6 15.9 + - - +
145A ALA* 3.8 5.0 + - - +
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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
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27A TYR 5.5 0.2 - - - +
30A ALA* 3.8 22.7 - - - +
31A MSE 4.0 13.2 + - - +
34A ARG* 2.8 37.8 + - - +
140A GLY 3.2 1.0 - - - -
141A ARG* 1.3 77.4 - - - +
143A VAL* 1.3 62.4 + - - +
145A ALA* 4.3 7.4 - - - -
146A VAL* 3.3 21.9 - - - +
73C TYR* 4.5 11.1 - - - -
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Residues in contact with VAL 143 (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 SER* 6.0 2.0 - - - +
127A ILE* 5.0 10.1 - - + -
128A ASP 6.1 0.2 - - - +
131A ARG* 4.2 31.5 - - + +
140A GLY* 2.9 31.3 + - - +
142A ASP* 1.3 80.4 - - - +
144A TYR* 1.3 74.0 + - + +
145A ALA 3.0 1.5 + - - -
146A VAL* 3.5 5.7 + - - +
147A VAL* 3.3 27.6 + - + +
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Residues in contact with TYR 144 (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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80A VAL* 3.6 31.4 - - + +
82A VAL* 3.4 35.0 - - + -
84A ASP* 5.2 3.1 + - + +
91A ARG 5.8 0.3 - - - -
92A LYS 4.7 0.2 + - - -
93A SER* 2.9 32.0 + - - -
105A VAL* 3.8 12.8 - - + +
106A GLY* 3.4 34.1 - - - -
107A PRO* 3.5 26.7 - - + +
127A ILE* 4.5 5.6 - - + -
140A GLY 3.9 22.0 - - - -
141A ARG 3.6 4.1 + - - +
143A VAL* 1.3 81.7 - - + +
145A ALA* 1.3 58.3 + - - +
147A VAL* 4.5 1.3 - - - -
148A GLY 3.1 21.1 + - - -
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Residues in contact with ALA 145 (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 MSE 3.8 31.2 - - + +
34A ARG* 4.8 9.6 - - + -
35A ILE* 4.0 22.7 - - + +
38A ILE* 5.4 0.2 - - - -
80A VAL* 4.6 5.3 - - - +
141A ARG 3.8 9.0 + - - +
142A ASP* 4.3 10.1 - - - +
143A VAL 3.0 0.2 - - - -
144A TYR* 1.3 77.5 - - - +
146A VAL* 1.3 66.7 + - - +
148A GLY* 3.3 1.6 + - - -
149A ALA* 3.0 23.4 + - - +
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Residues in contact with VAL 146 (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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34A ARG* 3.5 21.3 - - - +
38A ILE* 3.6 24.9 - - + +
131A ARG* 4.8 21.5 - - + +
142A ASP 3.3 22.7 - - - +
143A VAL* 3.5 7.3 + - - +
145A ALA* 1.3 73.9 - - - +
147A VAL* 1.3 53.6 + - - +
149A ALA* 3.2 3.1 + - - +
150A GLU* 2.8 41.8 + - + +
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Residues in contact with VAL 147 (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 VAL* 3.8 29.8 - - + -
105A VAL* 3.9 12.6 - - + -
127A ILE* 4.4 15.3 - - + -
131A ARG* 3.8 33.9 - - - +
143A VAL* 3.3 18.1 + - + +
144A TYR 3.9 4.0 - - - +
145A ALA 3.2 0.2 - - - -
146A VAL* 1.3 76.2 - - - +
148A GLY* 1.3 63.5 + - - +
150A GLU* 3.1 7.9 + - - +
151A ILE* 2.9 32.4 + - + +
157A TYR* 3.8 13.7 - - + +
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Residues in contact with GLY 148 (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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15A ILE* 3.6 20.8 - - - +
78A VAL* 3.8 14.9 - - - +
80A VAL* 4.2 3.4 - - - -
105A VAL* 4.3 1.6 - - - -
144A TYR 3.1 17.0 + - - -
145A ALA 3.3 3.5 + - - -
147A VAL* 1.3 76.4 - - - +
149A ALA* 1.3 60.2 + - - +
151A ILE* 3.6 8.4 + - - +
152A LEU* 3.3 23.6 + - - +
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Residues in contact with ALA 149 (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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15A ILE* 4.2 1.5 - - - +
35A ILE* 4.3 14.8 - - + +
38A ILE* 4.0 20.4 - - + -
39A LEU* 3.7 22.6 - - + +
145A ALA 3.0 15.9 + - - +
146A VAL 3.6 4.0 - - - +
148A GLY* 1.3 74.4 - - - +
150A GLU* 1.3 60.4 + - - +
152A LEU* 3.0 10.4 + - - +
153A ILE* 3.0 32.9 + - - +
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Residues in contact with GLU 150 (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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38A ILE* 5.1 1.5 - - + +
130A GLU* 3.9 8.1 - - - +
131A ARG* 2.4 33.7 + - - -
146A VAL* 2.8 22.2 + - + +
147A VAL* 3.3 4.0 - - - +
149A ALA* 1.3 78.4 - - - +
151A ILE* 1.3 55.9 + - - +
153A ILE* 3.3 9.8 + - - +
154A ASN* 3.0 45.4 + - - +
156A GLY 4.7 0.7 - - - +
157A TYR* 2.8 26.2 - - + -
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Residues in contact with ILE 151 (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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12A LEU* 3.7 13.6 - - + +
78A VAL* 3.7 18.6 - - + -
95A VAL* 3.9 21.5 - - + -
103A TYR* 3.8 20.0 - - + -
105A VAL* 3.6 30.1 - - + -
147A VAL* 2.9 25.0 + - + +
148A GLY* 3.7 7.6 - - - +
149A ALA 3.2 0.2 - - - -
150A GLU* 1.3 75.0 - - - +
152A LEU* 1.3 58.4 + - - +
155A ASN* 2.8 26.3 + - - -
156A GLY 3.0 22.3 + - - +
157A TYR* 3.7 19.1 - - + -
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Residues in contact with LEU 152 (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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11A ILE* 5.2 0.9 - - - +
12A LEU* 3.5 35.0 - - + +
13A ASP 4.0 2.5 - - - +
14A ILE 3.8 12.8 - - - +
15A ILE* 3.8 26.7 - - + -
35A ILE* 5.2 0.7 - - + -
39A LEU* 4.2 19.7 - - + -
44A LYS* 3.3 25.1 + - - -
46A ALA* 3.8 21.3 - - + -
78A VAL* 3.7 20.2 - - + -
148A GLY 3.3 13.6 + - - +
149A ALA* 3.0 9.5 + - - +
151A ILE* 1.3 81.7 - - - +
153A ILE* 1.3 61.2 + - - +
155A ASN* 3.7 7.3 + - - +
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Residues in contact with ILE 153 (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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38A ILE* 3.4 26.2 - - + +
39A LEU* 4.2 10.5 - - + -
42A TYR* 3.3 50.7 - - + -
44A LYS* 4.3 18.7 - - + +
149A ALA 3.0 13.4 + - - +
150A GLU* 3.7 10.1 - - - +
151A ILE 3.3 0.2 - - - -
152A LEU* 1.3 80.1 - - - +
154A ASN* 1.3 72.2 + - - +
155A ASN* 3.3 2.3 + - - +
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Residues in contact with ASN 154 (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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150A GLU* 3.0 31.8 + - - +
153A ILE* 1.3 90.6 + - - +
155A ASN* 1.3 71.2 + - - +
156A GLY* 3.1 13.2 + - - +
158A ASP* 6.0 1.3 - - - +
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Residues in contact with ASN 155 (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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10A ASP* 2.9 24.8 + - - +
11A ILE* 3.9 22.2 - - + +
12A LEU* 3.2 35.2 - - - +
103A TYR* 4.7 2.1 + - - -
151A ILE 2.8 11.9 + - - -
152A LEU 3.7 5.3 + - - +
153A ILE 3.3 4.5 - - - +
154A ASN* 1.3 79.9 - - - +
156A GLY* 1.3 56.1 + - - +
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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