Contacts of the helix formed by residues 199 - 213 (chain A) in PDB entry 4WPN
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 PRO 199 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 4.3 6.5 - - + -
40A VAL* 3.7 25.4 - - + -
52A VAL* 4.2 9.9 - - + -
110A ASN* 4.0 3.1 - - - +
194A PRO* 4.0 11.2 - - + +
195A ALA 3.4 8.5 - - - +
196A GLU 3.5 10.1 - - - +
197A GLN 3.4 7.2 - - - +
198A THR* 1.3 91.6 - - - +
200A LEU* 1.3 65.2 + - + +
201A THR 3.6 0.9 - - - -
202A ALA* 3.4 8.1 + - - +
203A LEU* 3.3 27.0 + - + +
223A PRO* 4.0 25.1 - - + -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.0 35.2 - - + -
20A TYR 4.2 12.1 - - - +
40A VAL* 4.1 11.4 - - + -
49A LEU* 4.4 6.1 - - + -
50A CYS* 3.7 24.2 - - - -
52A VAL* 3.9 18.8 - - + -
106A MET* 3.6 27.0 - - + +
110A ASN* 3.4 30.0 + - + +
198A THR 3.4 2.6 - - - -
199A PRO* 1.3 74.3 - - + +
201A THR* 1.3 66.3 + - - +
203A LEU* 3.1 7.1 + - + +
204A HIS* 3.1 17.8 + - - +
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.8 15.7 - - + +
106A MET* 3.8 18.8 - - + +
107A GLU* 2.8 51.7 + - - +
110A ASN* 4.9 2.4 + - + +
172A PRO* 3.8 14.6 - - - +
173A LEU* 4.0 18.7 + - + +
198A THR* 4.8 2.1 + - - -
200A LEU* 1.3 76.0 - - + +
202A ALA* 1.3 57.5 + - - +
204A HIS* 3.3 3.5 + - - +
205A VAL* 2.9 34.2 + - - +
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 6.3 0.2 - - + -
172A PRO 6.0 1.3 - - - +
176A LEU* 3.8 28.0 - - + +
194A PRO* 4.0 26.7 - - + -
198A THR 5.2 1.3 + - - +
199A PRO 3.4 12.0 + - - +
200A LEU 3.2 0.6 - - - -
201A THR* 1.3 81.8 + - - +
203A LEU* 1.3 57.0 + - - +
205A VAL* 3.3 2.6 + - - +
206A ALA 2.9 22.2 + - - -
221A ILE* 3.3 21.8 - - + +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.8 30.9 - - + +
21A THR* 4.0 11.9 - - - -
22A LYS 3.4 26.2 - - - +
24A PHE* 4.9 0.4 - - + -
29A TRP* 3.4 15.0 - - + -
52A VAL* 4.1 9.2 - - + -
199A PRO* 3.3 17.9 + - + +
200A LEU* 3.1 9.0 + - - +
202A ALA* 1.3 73.4 - - - +
204A HIS* 1.3 65.6 + - - +
206A ALA* 3.2 6.2 + - - +
207A SER* 3.2 16.6 + - - -
221A ILE* 3.7 29.8 - - + +
223A PRO* 4.0 22.4 - - + -
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Residues in contact with HIS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 4.9 5.3 + - - -
20A TYR* 3.8 27.1 - + + +
99A ASP* 2.7 31.9 + - - +
102A LEU* 3.7 28.2 - - + +
103A LEU* 3.5 28.3 - - + -
106A MET* 4.4 10.9 - - + +
200A LEU 3.1 12.6 + - - +
201A THR 3.3 6.9 + - - +
203A LEU* 1.3 77.3 - - - +
205A VAL* 1.3 60.9 + - - +
207A SER* 2.5 33.3 + - - -
208A LEU* 3.2 19.2 + - + +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 4.4 15.3 - - + -
96A ILE* 4.6 16.6 - - + -
103A LEU* 4.6 9.6 - - + -
173A LEU* 3.3 28.0 - - + -
176A LEU* 3.9 17.9 - - + -
177A ILE* 4.8 5.2 - - + -
180A ILE* 4.8 1.3 - - + -
201A THR 2.9 19.7 + - - +
202A ALA 3.3 7.4 + - - +
204A HIS* 1.3 74.4 - - - +
206A ALA* 1.3 56.8 + - - +
208A LEU* 2.8 25.8 + - - +
209A ILE* 2.8 29.7 + - + +
221A ILE* 5.8 0.4 - - + -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.4 38.0 - - + -
29A TRP* 4.0 3.1 - - + -
202A ALA 2.9 8.5 + - - +
203A LEU* 3.3 12.3 - - - +
204A HIS 3.1 0.2 - - - -
205A VAL* 1.3 76.3 - - - +
207A SER* 1.3 63.0 + - - +
209A ILE* 3.0 19.5 + - - +
210A LYS 3.1 10.2 + - - -
221A ILE* 3.4 28.2 - - + +
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.4 47.7 + - - -
29A TRP* 4.1 10.4 - - - -
203A LEU 3.2 2.6 + - - -
204A HIS* 2.5 22.8 + - - -
206A ALA* 1.3 78.3 - - - +
208A LEU* 1.3 65.7 + - - +
210A LYS* 3.5 8.2 + - - +
211A GLU* 3.1 25.1 + - - +
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.7 13.0 - - + +
95A LEU* 3.5 27.5 - - + +
96A ILE* 3.9 23.6 - - + -
98A ARG* 3.5 18.4 - - - +
99A ASP* 3.4 27.8 - - - +
103A LEU* 4.5 2.2 - - + -
204A HIS* 3.6 25.6 - - + +
205A VAL* 2.8 15.0 + - - +
207A SER* 1.3 75.1 - - - +
209A ILE* 1.3 59.0 + - - +
211A GLU* 3.6 12.1 - - - +
212A ALA* 2.8 31.2 + - - +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.5 9.2 - - + -
27A ASN* 4.6 4.5 - - - +
92A LEU* 3.8 22.2 - - + -
176A LEU* 6.3 0.2 - - + -
180A ILE* 4.1 19.5 - - + -
184A LEU* 5.5 0.2 - - + -
205A VAL* 2.8 21.9 + - + +
206A ALA* 3.4 14.8 - - - +
208A LEU* 1.3 76.1 - - - +
210A LYS* 1.3 63.1 + - - +
212A ALA 3.4 0.7 + - - -
213A GLY 3.3 16.6 + - - -
214A PHE* 3.4 39.5 + - + -
219A VAL* 3.7 45.1 - - + +
221A ILE* 4.9 2.7 - - + -
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Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.1 14.1 - - + -
27A ASN* 3.0 47.0 + - + +
28A GLU* 4.7 4.4 - - - +
29A TRP* 5.3 11.6 - - - +
206A ALA 3.1 10.1 + - - +
207A SER* 3.5 10.8 - - - +
209A ILE* 1.3 77.9 - - - +
211A GLU* 1.3 64.5 + - - +
213A GLY* 3.3 13.3 + - - -
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 5.5 3.8 - - - -
95A LEU* 3.8 13.2 - - + +
98A ARG* 2.8 44.1 + - - -
207A SER 3.1 14.3 + - - +
208A LEU* 3.6 17.9 - - - +
210A LYS* 1.3 76.1 - - - +
212A ALA* 1.3 62.3 + - - +
213A GLY* 3.3 1.6 + - - -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.3 16.4 - - + +
91A LYS* 4.0 24.0 - - + +
92A LEU* 4.3 8.1 - - - +
95A LEU* 3.9 14.8 - - + +
208A LEU 2.8 21.5 + - - +
209A ILE 3.8 4.9 - - - +
210A LYS 3.3 0.2 - - - -
211A GLU* 1.3 73.4 - - - +
213A GLY* 1.3 58.7 + - - +
214A PHE* 4.0 20.0 - - + -
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Residues in contact with GLY 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET* 5.8 0.3 - - - +
88A LEU* 3.6 12.7 - - - +
209A ILE 3.3 0.4 + - - -
210A LYS 3.3 11.3 + - - -
211A GLU 3.2 4.3 - - - -
212A ALA* 1.3 80.4 - - - +
214A PHE* 1.3 66.9 + - - +
215A PRO* 3.5 5.2 - - - +
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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