Contacts of the helix formed by residues 147 - 159 (chain P) in PDB entry 2X17
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 SER 147 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1484 PRO* 6.2 0.7 - - - -
1494 GLN* 3.5 10.2 + - - -
144P ALA* 3.6 19.2 + - - +
145P LYS 3.5 4.6 + - - -
146P ASP* 1.3 78.5 - - - +
148P PRO* 1.3 63.5 - - - +
149P GLN* 3.3 16.5 + - - -
150P ILE* 3.4 36.6 + - - +
151P LEU* 3.4 18.9 + - - +
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Residues in contact with PRO 148 (chain P).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146P ASP 3.9 5.8 - - - +
147P SER* 1.3 85.6 - - - +
149P GLN* 1.3 73.9 + - - +
151P LEU* 3.8 9.9 - - + -
152P PHE* 3.0 30.0 + - - +
143Z PHE* 3.6 35.0 - - + +
150Z ILE* 4.0 11.1 - - + +
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Residues in contact with GLN 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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1494 GLN* 3.8 28.2 + - + -
146P ASP 5.2 0.3 - - - +
147P SER* 3.3 17.3 + - - +
148P PRO* 1.3 94.9 - - - +
150P ILE* 1.3 61.2 + - - +
152P PHE* 3.5 5.0 + - - +
153P MET* 3.3 29.8 + - + +
146Z ASP 5.5 0.6 + - - -
147Z SER* 3.1 34.2 + - - +
149Z GLN* 3.8 21.7 + - + +
150Z ILE* 3.8 17.5 - - + +
153Z MET* 4.2 6.6 - - + +
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Residues in contact with ILE 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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1484 PRO* 3.8 38.4 - - + +
1494 GLN* 4.1 17.3 - - + +
1524 PHE* 4.0 29.2 - - + -
140P LYS 5.0 2.0 - - - +
143P PHE* 4.5 10.8 - - + +
144P ALA* 3.7 24.7 - - + -
147P SER* 3.4 24.2 + - - +
149P GLN* 1.3 74.6 - - - +
151P LEU* 1.3 60.9 + - - +
153P MET* 3.3 11.1 + - + -
154P LEU* 2.8 35.4 + - + +
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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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36P LEU* 4.2 15.7 - - + +
39P PHE* 4.1 14.4 - - + -
83P PRO* 4.3 23.8 - - + -
141P LEU* 3.8 28.9 - - + -
144P ALA* 4.8 4.8 - - + +
147P SER 3.4 15.7 + - - +
148P PRO* 3.7 8.7 - - + +
149P GLN 3.3 0.4 - - - -
150P ILE* 1.3 78.3 - - - +
152P PHE* 1.3 59.8 + - - +
154P LEU* 3.5 7.9 + - + +
155P ASP* 3.1 21.8 + - - +
143Z PHE* 3.6 26.0 - - + -
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Residues in contact with PHE 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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36P LEU* 5.6 1.6 - - - -
148P PRO 3.0 18.8 + - - +
149P GLN 3.6 4.9 - - - +
151P LEU* 1.3 77.7 - - - +
153P MET* 1.3 60.8 + - + +
155P ASP* 3.4 21.4 + - + +
156P LYS* 3.5 10.6 + - + +
140Z LYS* 4.5 26.9 - - + -
143Z PHE* 4.4 16.3 - + + -
150Z ILE* 4.0 22.2 - - + -
153Z MET* 3.7 47.3 - - + -
154Z LEU* 4.6 10.5 - - + -
157Z GLU* 3.7 35.0 - - - -
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Residues in contact with MET 153 (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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1494 GLN* 4.2 13.5 - - + +
1524 PHE* 3.7 33.8 - - + -
1534 MET* 3.8 20.6 - - + -
11744 AG 2.8 28.5 - - - -
149P GLN* 3.3 20.5 + - + +
150P ILE* 3.3 16.7 + - + +
152P PHE* 1.3 76.3 - - + +
154P LEU* 1.3 63.3 + - - +
155P ASP 3.3 0.2 - - - -
156P LYS* 3.7 8.1 + - - +
157P GLU* 3.4 26.2 + - - +
153Z MET* 3.7 18.2 - - + +
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Residues in contact with LEU 154 (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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1524 PHE* 4.6 9.6 - - + -
39P PHE* 3.9 10.8 - - + -
137P ILE* 4.8 14.1 - - + -
140P LYS* 3.8 54.7 - - + +
141P LEU* 4.4 18.4 - - + -
144P ALA* 5.2 1.6 - - + -
150P ILE* 2.8 27.1 + - + +
151P LEU* 3.8 8.7 - - + +
152P PHE 3.3 0.2 - - - -
153P MET* 1.3 73.6 - - - +
155P ASP* 1.3 65.5 + - - +
157P GLU* 3.3 15.8 + - + +
158P LEU* 3.2 36.2 + - + +
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Residues in contact with ASP 155 (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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35P GLY 4.7 2.1 - - - +
36P LEU* 3.2 21.4 - - + -
37P GLU* 3.7 9.6 + - - +
38P GLY* 2.9 41.3 + - - -
39P PHE* 3.2 25.1 + - + -
151P LEU 3.1 13.9 + - - +
152P PHE* 3.5 16.3 - - + +
153P MET 3.3 0.2 - - - -
154P LEU* 1.3 77.6 - - - +
156P LYS* 1.3 60.7 + - - +
158P LEU 3.5 1.2 + - - -
159P SER* 3.2 18.0 + - - -
140Z LYS* 5.6 5.9 + - - -
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Residues in contact with LYS 156 (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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1564 LYS* 5.0 12.9 - - - +
152P PHE* 3.5 11.3 + - + +
153P MET* 3.7 10.3 + - - +
154P LEU 3.3 0.2 - - - -
155P ASP* 1.3 78.9 - - - +
157P GLU* 1.3 61.6 + - + +
159P SER* 2.6 26.0 + - - +
160P ALA* 4.1 2.6 + - - +
156Z LYS* 5.5 8.7 - - - +
157Z GLU* 3.9 29.3 + - - +
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Residues in contact with GLU 157 (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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1524 PHE* 3.3 31.6 - - + -
1564 LYS* 4.5 25.1 - - + +
140P LYS* 3.6 23.0 + - - -
153P MET 3.4 10.0 + - - +
154P LEU* 3.3 15.7 + - + +
155P ASP 3.3 0.6 - - - -
156P LYS* 1.3 79.7 - - + +
158P LEU* 1.3 65.0 + - + +
159P SER 3.6 0.3 + - - -
160P ALA* 3.7 17.0 - - - +
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Residues in contact with LEU 158 (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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38P GLY 3.4 19.9 - - - +
39P PHE* 3.6 42.6 - - + -
42P TRP* 3.7 30.5 - - + +
87P PHE* 4.9 1.8 - - + -
137P ILE* 3.8 34.1 - - + -
154P LEU* 3.2 19.4 + - + +
155P ASP 4.2 0.2 - - - +
156P LYS 3.3 0.2 - - - -
157P GLU* 1.3 77.9 - - + +
159P SER* 1.3 60.1 + - - +
160P ALA 3.1 5.8 - - - -
161P ARG* 3.2 24.5 + - - +
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Residues in contact with SER 159 (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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37P GLU 5.4 0.2 - - - -
38P GLY* 3.8 16.4 - - - -
41P ASN* 5.2 9.1 + - - -
155P ASP* 3.2 14.5 + - - -
156P LYS* 2.6 28.4 + - - +
158P LEU* 1.3 75.2 - - - +
160P ALA* 1.3 62.0 + - - +
161P ARG 3.2 8.3 + - - +
162P ALA* 4.7 6.1 - - - +
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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