Contacts of the helix formed by residues 141 - 154 (chain B) 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 ARG 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A SER* 4.2 27.7 + - - +
21B PHE* 6.2 2.9 - - + -
31B MSE 4.3 14.2 - - + +
82B VAL* 5.1 4.6 - - + +
142B ASP* 1.3 89.0 + - + +
143B VAL* 2.9 24.8 + - - +
144B TYR* 3.3 37.2 + - - +
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 4.5 19.8 + - - -
30B ALA* 5.2 4.5 - - - +
31B MSE 4.1 25.8 + - - +
34B ARG* 4.8 13.7 - - + +
141B ARG* 1.3 100.8 + - + +
143B VAL* 1.3 64.1 + - - +
144B TYR 3.4 0.4 - - - -
145B ALA* 3.7 10.1 + - - +
146B VAL* 3.4 24.7 + - + +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER* 5.8 1.6 - - - +
127B ILE* 4.0 17.5 - - + -
131B ARG* 3.9 33.0 - - + -
141B ARG 2.9 15.4 - - - +
142B ASP* 1.3 78.9 - - - +
144B TYR* 1.3 74.0 + - + +
146B VAL* 3.1 8.2 + - - +
147B VAL* 2.9 41.5 + - + +
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B MSE 5.8 0.2 - - - -
80B VAL* 3.8 22.3 - - + +
82B VAL* 3.6 34.8 - - + -
84B ASP* 5.6 2.4 - - + +
92B LYS 4.6 0.7 + - - -
93B SER* 3.4 22.5 - - - -
105B VAL* 3.6 14.2 - - + +
106B GLY* 3.4 33.4 - - - -
107B PRO* 3.3 31.9 - - + +
127B ILE* 4.5 7.9 - - + -
141B ARG* 3.3 28.0 + - - +
143B VAL* 1.3 82.4 - - + +
145B ALA* 1.3 63.1 + - - +
147B VAL* 4.5 1.1 - - - -
148B GLY* 3.0 20.6 + - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B MSE 3.8 27.2 - - + +
34B ARG* 4.2 14.4 - - + -
35B ILE* 3.5 33.4 - - + +
80B VAL* 4.5 4.2 - - - +
141B ARG 4.4 0.8 + - - -
142B ASP* 3.7 15.0 + - - +
143B VAL 3.2 0.6 - - - -
144B TYR* 1.3 78.6 - - - +
146B VAL* 1.3 62.8 + - - +
148B GLY* 3.2 2.8 + - - -
149B ALA* 3.1 18.4 + - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 3.8 19.1 - - + -
38B ILE* 3.5 31.1 - - + +
131B ARG* 3.9 26.7 - - + +
142B ASP* 3.4 13.4 + - + +
143B VAL* 3.1 9.7 + - - +
145B ALA* 1.3 75.7 - - - +
147B VAL* 1.3 67.7 + - - +
149B ALA* 3.0 4.0 + - - +
150B GLU* 2.8 24.7 + - + +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 3.7 30.1 - - + -
105B VAL* 4.2 9.2 - - + -
127B ILE* 4.0 10.3 - - + -
131B ARG* 3.7 25.4 - - - +
143B VAL* 2.9 41.0 + - + +
144B TYR 3.8 3.8 - - - +
146B VAL* 1.3 73.7 - - - +
148B GLY* 1.3 62.2 + - - +
150B GLU* 3.3 8.0 + - - +
151B ILE* 3.0 34.9 + - + +
157B TYR* 4.0 14.6 - - + -
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.8 17.3 - - - -
78B VAL* 4.0 7.3 - - - +
80B VAL* 4.3 1.6 - - - -
105B VAL* 4.0 17.2 - - - +
144B TYR 3.0 14.9 + - - -
145B ALA 3.7 3.8 - - - -
147B VAL* 1.3 76.7 - - - +
149B ALA* 1.3 61.3 + - - +
151B ILE* 3.3 12.4 + - - +
152B LEU* 3.3 15.6 + - - +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.1 3.0 - - - +
35B ILE* 4.2 11.7 - - + +
38B ILE* 3.6 23.6 - - + -
39B LEU* 3.5 25.5 - - + +
145B ALA 3.1 10.9 + - - +
146B VAL 3.0 8.0 + - - +
148B GLY* 1.3 72.1 - - - +
150B GLU* 1.3 67.3 + - - +
152B LEU* 2.8 19.4 + - - +
153B ILE* 3.1 17.3 + - - +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 4.8 2.4 - - + +
131B ARG* 5.2 4.9 - - - +
146B VAL* 2.8 17.1 + - + +
147B VAL* 3.4 14.1 - - - +
149B ALA* 1.3 77.7 - - - +
151B ILE* 1.3 62.8 + - + +
152B LEU 3.2 0.2 + - - -
153B ILE* 3.2 11.1 + - - +
154B ASN* 2.9 36.5 + - - +
156B GLY 4.6 0.9 - - - -
157B TYR* 5.1 10.1 - - + -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 3.5 21.1 - - + +
78B VAL* 4.0 7.2 - - + -
95B VAL* 3.8 28.9 - - + -
103B TYR* 3.7 22.7 - - + -
105B VAL* 3.8 20.6 - - + -
147B VAL* 3.0 19.4 + - + +
148B GLY* 3.5 7.4 - - - +
149B ALA 3.2 0.4 - - - -
150B GLU* 1.3 76.0 - - - +
152B LEU* 1.3 57.6 + - - +
155B ASN* 2.8 23.4 + - - -
156B GLY 2.9 25.0 + - - +
157B TYR* 3.7 20.4 - - + -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 3.8 36.6 - - + +
13B ASP 4.3 0.9 - - - +
14B ILE 4.3 8.3 - - - +
15B ILE* 3.8 29.6 - - + -
39B LEU* 4.0 16.2 - - + -
44B LYS* 3.1 29.3 + - + -
46B ALA* 3.5 30.5 - - + -
78B VAL* 3.9 14.8 - - + -
148B GLY 3.3 8.4 + - - +
149B ALA* 2.8 9.0 + - - +
151B ILE* 1.3 76.2 - - - +
153B ILE* 1.3 65.8 + - - +
155B ASN* 3.3 11.4 + - - +
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.4 34.5 - - + +
39B LEU* 4.2 4.7 - - + -
42B TYR* 3.5 52.0 - - + +
44B LYS* 3.9 26.8 - - + +
149B ALA 3.1 13.2 + - - +
150B GLU* 3.8 6.7 - - - +
152B LEU* 1.3 78.2 - - - +
154B ASN* 1.3 67.1 + - - +
155B ASN* 3.2 5.5 + - - +
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Residues in contact with ASN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B TYR* 5.4 5.5 - - - -
150B GLU* 2.9 20.8 + - - +
153B ILE* 1.3 89.0 - - - +
155B ASN* 1.3 70.2 + - - +
156B GLY* 3.2 14.0 + - - +
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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