Contacts of the helix formed by residues 147 - 159 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1491 GLN* 3.4 20.3 + - - +
144I ALA* 4.0 16.5 + - - +
145I LYS 3.5 4.4 + - - -
146I ASP* 1.3 79.4 - - - +
148I PRO* 1.3 64.1 - - - +
149I GLN* 3.1 15.3 + - - -
150I ILE* 3.4 29.9 + - - +
151I LEU* 3.5 17.2 + - - +
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Residues in contact with PRO 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437 PHE* 3.7 34.0 - - + +
1477 SER* 6.4 0.2 - - - -
1507 ILE* 4.1 10.3 - - + -
146I ASP 4.0 6.3 - - - +
147I SER* 1.3 84.9 - - - +
149I GLN* 1.3 73.5 + - - +
150I ILE 3.3 0.2 - - - -
151I LEU* 3.6 11.1 - - + +
152I PHE* 2.9 30.7 + - - +
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Residues in contact with GLN 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491 GLN* 4.2 20.7 + - + +
1477 SER* 2.9 27.9 + - - +
1497 GLN* 3.6 23.9 + - + +
1507 ILE* 3.8 24.8 - - + +
1537 MET* 4.2 8.1 - - + +
146I ASP 5.2 0.2 - - - +
147I SER* 3.1 17.1 + - - +
148I PRO* 1.3 91.6 - - - +
150I ILE* 1.3 60.2 + - - +
152I PHE* 3.6 3.2 + - - +
153I MET* 3.2 31.2 + - + +
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Residues in contact with ILE 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1481 PRO* 4.1 34.3 - - + +
1491 GLN* 4.0 19.1 - - + +
1521 PHE* 4.4 24.2 - - + -
140I LYS* 4.8 2.9 - - + +
143I PHE* 4.4 9.0 - - + +
144I ALA* 3.6 28.0 - - + -
147I SER* 3.4 25.8 + - - +
148I PRO 3.3 0.2 - - - -
149I GLN* 1.3 74.6 - - - +
151I LEU* 1.3 55.3 + - - +
153I MET* 3.2 9.3 + - + +
154I LEU* 2.8 45.6 + - + +
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Residues in contact with LEU 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437 PHE* 3.8 24.0 - - + -
36I LEU* 4.4 16.3 - - + +
39I PHE* 4.1 15.1 - - + -
83I PRO* 4.4 22.9 - - + -
141I LEU* 3.8 28.3 - - + -
144I ALA* 4.8 5.0 - - + +
147I SER 3.5 12.2 + - - +
148I PRO* 3.3 10.5 + - + +
150I ILE* 1.3 78.3 - - - +
152I PHE* 1.3 56.6 + - - +
154I LEU* 3.7 7.2 - - + +
155I ASP* 3.1 26.2 + - - +
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Residues in contact with PHE 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1407 LYS* 4.6 25.6 - - + -
1437 PHE* 4.6 16.1 - + + -
1507 ILE* 4.2 21.1 - - + -
1537 MET* 3.9 43.3 - - + -
1547 LEU* 4.8 8.7 - - + -
1577 GLU* 3.3 38.4 - - - -
36I LEU* 5.6 2.5 - - + -
148I PRO 2.9 17.7 + - - +
149I GLN* 3.7 5.4 - - - +
150I ILE 3.2 0.2 - - - -
151I LEU* 1.3 76.1 - - - +
153I MET* 1.3 63.1 + - + +
155I ASP* 3.4 19.1 + - + +
156I LYS* 3.4 13.2 + - + +
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Residues in contact with MET 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491 GLN* 4.1 21.3 - - + +
1521 PHE* 3.9 30.9 - - + -
1531 MET* 3.9 11.4 - - + -
11741 AG 2.9 28.9 - - - -
1537 MET* 3.7 20.4 - - + +
149I GLN* 3.2 25.3 + - + +
150I ILE* 3.2 11.2 + - + +
152I PHE* 1.3 76.2 - - + +
154I LEU* 1.3 63.7 + - - +
156I LYS* 3.6 8.8 + - + +
157I GLU* 3.3 27.1 + - - +
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Residues in contact with LEU 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521 PHE* 4.8 7.1 - - + -
39I PHE* 4.1 9.9 - - + -
137I ILE* 4.6 16.2 - - + -
140I LYS* 3.9 51.4 - - + +
141I LEU* 4.2 20.9 - - + -
144I ALA* 5.2 1.6 - - + -
150I ILE* 2.8 34.5 + - + +
151I LEU* 3.7 8.5 - - - +
153I MET* 1.3 72.5 - - - +
155I ASP* 1.3 62.9 + - - +
157I GLU* 3.3 14.8 + - - +
158I LEU* 3.1 36.8 + - + +
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Residues in contact with ASP 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1407 LYS* 5.9 3.1 + - - -
35I GLY 4.6 2.6 - - - +
36I LEU* 3.3 25.2 - - + -
37I GLU* 3.7 7.6 + - - +
38I GLY* 2.9 40.4 + - - -
39I PHE* 3.2 25.5 + - + +
151I LEU 3.1 13.9 + - - +
152I PHE* 3.4 17.5 - - + +
153I MET 3.3 0.4 - - - -
154I LEU* 1.3 77.7 - - - +
156I LYS* 1.3 60.7 + - - +
158I LEU 3.5 0.3 + - - -
159I SER* 3.2 18.2 + - - -
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Residues in contact with LYS 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561 LYS* 4.8 15.5 - - - +
1567 LYS* 5.3 9.7 - - - +
1577 GLU* 4.4 24.7 - - - +
152I PHE* 3.4 10.6 + - + +
153I MET* 3.8 11.4 - - + +
154I LEU 3.3 0.6 - - - -
155I ASP* 1.3 79.1 + - - +
157I GLU* 1.3 63.5 + - + +
159I SER* 2.6 26.8 + - - +
160I ALA* 4.0 2.6 + - - +
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Residues in contact with GLU 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521 PHE* 3.3 36.2 - - + -
1561 LYS* 4.5 26.0 - - + +
140I LYS* 4.0 16.7 + - - -
153I MET 3.3 11.6 + - - +
154I LEU* 3.3 15.5 + - + +
156I LYS* 1.3 79.3 - - + +
158I LEU* 1.3 66.2 + - + +
160I ALA* 3.5 19.9 - - - +
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Residues in contact with LEU 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I GLY 3.4 21.0 - - - +
39I PHE* 3.6 46.4 - - + -
42I TRP* 3.8 30.0 - - + +
87I PHE* 4.9 1.3 - - + -
137I ILE* 4.0 30.5 - - + -
154I LEU* 3.1 19.7 + - + +
156I LYS 3.3 0.2 - - - -
157I GLU* 1.3 76.8 - - + +
159I SER* 1.3 60.6 + - - +
160I ALA 3.1 6.1 - - - -
161I ARG* 3.2 24.5 + - - +
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Residues in contact with SER 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I GLU 5.4 0.2 - - - -
38I GLY* 3.9 14.6 - - - -
41I ASN* 5.2 7.9 + - - -
155I ASP 3.2 14.1 + - - -
156I LYS* 2.6 28.2 + - - +
158I LEU* 1.3 74.7 - - - +
160I ALA* 1.3 62.0 + - - +
161I ARG 3.2 8.2 + - - +
162I ALA* 4.9 4.5 - - - +
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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