Contacts of the helix formed by residues 147 - 159 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1499 GLN* 3.2 19.4 + - - -
144K ALA* 3.9 17.5 + - - +
145K LYS 3.5 3.2 - - - -
146K ASP* 1.3 77.7 - - - +
148K PRO* 1.3 62.8 - - - +
149K GLN* 2.9 18.3 + - - -
150K ILE* 3.4 29.0 + - - +
151K LEU* 3.3 19.9 + - - +
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Residues in contact with PRO 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1433 PHE* 3.8 34.4 - - + +
1503 ILE* 4.2 14.3 - - + +
146K ASP 3.4 11.0 - - - +
147K SER* 1.3 82.1 - - - +
149K GLN* 1.3 72.6 + - - +
150K ILE 3.4 0.2 - - - -
151K LEU* 3.8 10.6 - - + +
152K PHE* 3.1 29.3 + - - +
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Residues in contact with GLN 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473 SER* 3.6 29.1 + - - +
1493 GLN* 3.7 22.7 + - + +
1503 ILE* 4.1 15.4 - - + +
1533 MET* 4.1 7.6 - - + +
1499 GLN* 4.1 22.8 + - + -
147K SER* 2.9 22.5 + - - +
148K PRO* 1.3 93.6 - - - +
150K ILE* 1.3 58.4 + - - +
152K PHE* 3.6 3.9 + - - +
153K MET* 3.3 33.5 + - + +
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Residues in contact with ILE 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489 PRO* 4.0 18.8 - - + +
1499 GLN* 3.9 37.9 - - + +
1529 PHE* 4.0 31.6 - - + -
140K LYS 5.0 2.0 - - - +
143K PHE* 4.6 9.4 - - + +
144K ALA* 3.7 23.6 - - + -
147K SER* 3.4 24.9 + - - +
149K GLN* 1.3 74.5 - - - +
151K LEU* 1.3 60.1 + - - +
152K PHE 3.2 0.4 - - - -
153K MET* 3.2 9.9 + - + +
154K LEU* 2.8 35.6 + - + +
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Residues in contact with LEU 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1433 PHE* 3.9 26.2 - - + -
36K LEU* 4.5 21.2 - - + +
39K PHE* 4.1 14.2 - - + -
83K PRO* 4.4 18.6 - - + -
141K LEU* 3.8 28.0 - - + -
144K ALA* 4.6 6.8 - - + +
147K SER 3.3 16.5 + - - +
148K PRO* 3.9 6.7 - - + +
150K ILE* 1.3 77.0 - - - +
152K PHE* 1.3 61.5 + - - +
154K LEU* 3.5 7.8 + - - +
155K ASP* 3.2 21.5 + - - +
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Residues in contact with PHE 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403 LYS* 4.6 23.3 - - + -
1433 PHE* 5.3 10.7 - + + -
1503 ILE* 4.4 20.2 - - + -
1533 MET* 3.8 49.6 - - + -
1543 LEU* 4.8 9.0 - - + -
1573 GLU* 3.3 35.7 - - - -
36K LEU* 5.6 3.6 - - + -
148K PRO 3.1 19.1 + - - +
149K GLN* 3.7 4.9 - - - +
150K ILE 3.2 0.2 - - - -
151K LEU* 1.3 76.7 - - - +
153K MET* 1.3 63.8 + - + +
155K ASP* 3.3 23.3 + - + +
156K LYS* 3.5 11.2 + - + +
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Residues in contact with MET 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1533 MET* 3.9 19.3 - - + +
11723 AG 3.1 25.8 - - - -
1499 GLN* 4.3 12.3 - - + +
1529 PHE* 3.8 26.9 - - + -
1539 MET* 3.8 22.4 - - + +
149K GLN* 3.3 27.5 + - + +
150K ILE* 3.2 17.5 + - + +
152K PHE* 1.3 77.1 - - + +
154K LEU* 1.3 63.5 + - - +
156K LYS* 3.6 7.5 + - - +
157K GLU* 3.5 25.3 + - - +
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Residues in contact with LEU 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1529 PHE* 4.4 11.0 - - + -
39K PHE* 4.1 10.1 - - + -
137K ILE* 4.7 14.6 - - + -
140K LYS* 3.7 54.5 - - + +
141K LEU* 4.4 17.9 - - + -
144K ALA* 5.3 2.0 - - + -
150K ILE* 2.8 26.9 + - + +
151K LEU* 3.7 8.1 - - - +
152K PHE 3.3 0.2 - - - -
153K MET* 1.3 76.3 - - - +
155K ASP* 1.3 64.2 + - - +
157K GLU* 3.3 15.6 + - - +
158K LEU* 3.1 36.4 + - + +
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Residues in contact with ASP 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403 LYS* 5.4 6.4 + - - -
35K GLY 4.6 2.6 - - - +
36K LEU* 3.3 24.1 - - + -
37K GLU* 3.9 5.9 + - - +
38K GLY* 3.0 40.2 + - - -
39K PHE* 3.2 26.2 + - + +
151K LEU 3.2 13.9 + - - +
152K PHE* 3.4 17.2 - - + +
153K MET 3.3 0.2 - - - -
154K LEU* 1.3 78.1 - - - +
156K LYS* 1.3 61.5 + - - +
158K LEU 3.5 0.7 + - - -
159K SER* 3.2 18.0 + - - -
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Residues in contact with LYS 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563 LYS* 5.1 12.7 - - - +
1573 GLU* 4.6 23.4 - - + +
1569 LYS* 5.4 9.1 - - - +
152K PHE* 3.5 11.1 + - + +
153K MET* 3.9 9.4 - - - +
154K LEU 3.3 0.4 - - - -
155K ASP* 1.3 77.9 + - - +
157K GLU* 1.3 63.4 + - + +
159K SER* 2.6 25.1 + - - +
160K ALA* 4.0 3.8 + - - +
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Residues in contact with GLU 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1529 PHE* 3.4 35.0 - - - -
1569 LYS* 4.6 25.5 - - + +
140K LYS* 4.2 16.1 + - - -
153K MET 3.5 9.1 + - - +
154K LEU* 3.3 16.8 + - + +
156K LYS* 1.3 80.2 - - + +
158K LEU* 1.3 65.5 + - + +
160K ALA* 3.5 19.7 - - - +
161K ARG 4.8 0.2 + - - -
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Residues in contact with LEU 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K GLY 3.4 20.8 - - - +
39K PHE* 3.6 46.9 - - + -
42K TRP* 3.6 29.4 - - + +
87K PHE* 4.9 1.3 - - + -
137K ILE* 3.8 33.7 - - + -
154K LEU* 3.1 20.4 + - + +
155K ASP 3.5 0.9 + - - +
156K LYS 3.3 0.2 - - - -
157K GLU* 1.3 77.2 - - + +
159K SER* 1.3 59.1 + - - +
160K ALA 3.1 5.8 - - - -
161K ARG* 3.2 24.1 + - - +
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Residues in contact with SER 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K GLU 5.3 0.2 - - - -
38K GLY* 3.7 15.9 - - - -
41K ASN* 5.2 9.8 + - - -
155K ASP 3.2 14.3 + - - -
156K LYS* 2.6 30.5 + - - +
158K LEU* 1.3 74.1 - - - +
160K ALA* 1.3 61.4 + - - +
161K ARG 3.2 8.9 + - - +
162K ALA* 4.5 6.4 - - - +
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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