Contacts of the helix formed by residues 139 - 152 (chain P) in PDB entry 3FKS
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 THR 139 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140P PHE* 1.3 61.6 + - - +
141P GLN* 3.4 9.3 + - + +
142P GLU* 2.9 61.5 + - + +
143P SER* 3.3 7.8 + - - -
219P LEU* 5.1 3.4 - - - -
222P MET* 5.6 7.2 - - - +
37R ARG* 3.8 25.0 + - - +
39R GLN 5.5 0.2 - - - +
40R THR* 4.2 17.7 - - - -
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Residues in contact with PHE 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P MET* 5.9 0.2 - - + -
139P THR* 1.3 74.8 + - - +
141P GLN* 1.3 61.3 + - - +
143P SER* 3.2 9.2 + - - -
144P ALA* 3.1 24.5 + - - +
215P ALA 4.6 2.1 - - - +
216P ASN* 5.5 6.1 - - - +
219P LEU* 4.2 14.5 - - + +
17Q PRO* 3.9 28.0 - - + +
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Residues in contact with GLN 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139P THR* 3.1 11.2 + - + +
140P PHE* 1.3 76.0 - - - +
142P GLU* 1.3 63.5 + - - +
144P ALA* 3.3 7.7 - - - +
145P LEU* 2.9 37.2 + - + +
37R ARG 4.6 10.8 - - - +
38R SER* 5.1 10.3 - - - +
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Residues in contact with GLU 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P ILE* 3.0 42.4 - - + +
139P THR* 2.9 38.5 + - + +
141P GLN* 1.3 78.8 - - - +
143P SER* 1.3 62.8 + - - +
145P LEU* 3.0 15.1 + - - +
146P ILE* 2.9 35.7 + - + +
222P MET* 4.9 8.7 - - - +
40R THR* 4.8 11.9 - - - -
41R ASP 4.1 10.9 - - - +
42R ALA* 4.5 9.6 - - + +
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Residues in contact with SER 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139P THR 3.3 4.7 + - - -
140P PHE 3.2 10.0 + - - -
142P GLU* 1.3 79.0 - - - +
144P ALA* 1.3 59.9 + - - +
146P ILE* 3.7 10.1 - - - -
147P ALA* 2.8 27.7 + - - +
215P ALA 3.3 5.9 + - - -
218P MET* 2.9 37.9 - - - +
219P LEU* 3.3 27.1 - - - +
222P MET* 4.1 11.0 - - - -
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Residues in contact with ALA 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140P PHE 3.1 20.2 + - - +
141P GLN* 3.3 10.5 - - - +
143P SER* 1.3 77.2 + - - +
145P LEU* 1.3 54.8 + - + +
147P ALA* 3.7 2.1 - - - +
148P ASP* 2.7 36.4 + - - +
215P ALA* 3.9 19.2 + - + +
14R LEU* 4.2 23.1 - - + +
15R ASN* 6.0 0.7 - - - -
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Residues in contact with LEU 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141P GLN* 2.9 28.5 + - + +
142P GLU* 3.0 9.6 + - + +
144P ALA* 1.3 75.5 - - + +
146P ILE* 1.3 68.8 + - + +
148P ASP* 3.1 10.1 + - + +
149P LYS* 2.9 33.9 + - + +
14R LEU 5.4 4.7 - - - +
15R ASN* 6.1 2.9 - - - -
40R THR 6.2 0.4 - - - +
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Residues in contact with ILE 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P ILE* 3.7 22.4 - - + -
130P ILE* 4.1 35.9 - - + -
133P ILE* 4.8 7.9 - - + -
142P GLU* 2.9 27.9 + - + +
143P SER* 3.5 13.0 - - - +
145P LEU* 1.3 76.7 - - + +
147P ALA* 1.3 57.7 + - - +
149P LYS* 3.1 10.1 + - - +
150P LEU* 2.8 28.7 + - + +
218P MET* 3.8 11.7 - - + -
222P MET* 4.0 10.3 - - + -
42R ALA* 5.2 7.2 - - + -
43R PHE 6.0 0.4 - - - +
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Residues in contact with ALA 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P SER 2.8 19.4 + - - +
144P ALA 3.7 0.2 - - - +
146P ILE* 1.3 70.9 - - - +
148P ASP* 1.3 56.9 + - - +
150P LEU* 2.8 9.2 + - - +
151P LEU* 2.6 38.8 + - + +
211P GLU 5.3 1.3 - - - +
214P LEU* 3.3 29.1 - - + +
215P ALA* 3.6 18.8 - - + -
218P MET* 3.3 9.3 - - + +
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Residues in contact with ASP 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144P ALA 2.7 21.4 + - - +
145P LEU* 3.1 14.3 + - + +
147P ALA* 1.3 73.1 - - - +
149P LYS* 1.3 63.5 + - + +
151P LEU* 4.0 5.0 - - - +
152P SER* 2.8 41.9 + - - -
11R ALA 3.2 9.7 - - - +
12R ALA* 3.2 39.3 + - - +
14R LEU 3.3 17.0 - - - +
15R ASN* 5.4 0.3 - - - +
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Residues in contact with LYS 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P LEU* 4.9 8.0 - - + +
145P LEU* 2.9 20.5 + - + +
146P ILE* 3.5 9.0 - - - +
148P ASP* 1.3 80.9 - - - +
150P LEU* 1.3 59.7 + - - +
151P LEU 3.4 0.7 - - - -
152P SER* 4.0 7.4 - - - +
153P VAL* 2.9 46.2 + - + +
154P MET* 3.5 3.3 + - - +
44R TYR* 5.1 19.7 - - + -
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Residues in contact with LEU 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P VAL* 4.8 20.2 - - + -
108P VAL* 4.0 28.0 - - + -
128P LEU* 5.5 2.0 - - + -
146P ILE* 2.8 15.5 + - + +
147P ALA* 2.8 12.4 + - - +
149P LYS* 1.3 78.4 - - - +
151P LEU* 1.3 59.1 + - - +
154P MET* 3.2 41.9 - - + +
155P LYS 3.2 6.6 + - - -
156P ALA* 3.3 26.4 + - + +
162P ILE* 6.3 1.3 - - + -
214P LEU* 4.8 21.1 - - + -
218P MET* 5.2 8.1 - - - -
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Residues in contact with LEU 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147P ALA* 2.6 19.1 + - + +
148P ASP* 4.0 4.0 - - - +
150P LEU* 1.3 73.3 - - - +
152P SER* 1.3 66.7 + - - +
155P LYS* 3.1 20.4 + - - +
156P ALA 4.7 2.0 - - - +
157P GLY 6.0 0.2 - - - +
211P GLU* 3.8 11.9 - - - +
214P LEU* 6.4 0.9 - - + -
11R ALA* 3.5 33.2 - - + -
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Residues in contact with SER 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P ASP* 2.8 31.9 + - - -
149P LYS* 4.5 6.5 - - - -
151P LEU* 1.3 79.1 - - - +
153P VAL* 1.3 62.4 + - - +
154P MET 2.8 10.1 + - - -
155P LYS* 3.3 19.2 - - - +
11R ALA* 5.4 1.8 - - - +
12R ALA* 4.9 8.0 + - - +
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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