Contacts of the helix formed by residues 201 - 216 (chain A) in PDB entry 2JPD
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLN* 3.6 12.9 + - - +
173A VAL 5.2 1.1 - - - -
199A ALA* 3.2 6.5 + - - +
200A TRP* 1.3 82.6 - - - +
202A PRO* 1.4 73.8 - - - +
203A GLU* 3.0 23.1 + - - +
204A GLU* 3.1 28.2 + - - +
205A ALA 3.2 15.8 + - - -
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Residues in contact with PRO 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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111A PRO* 3.8 35.2 - - + -
112A VAL* 3.6 12.2 - - + +
115A PHE* 3.4 18.5 - - + -
172A GLN* 3.1 26.0 - - + +
201A SER* 1.4 85.6 - - - +
203A GLU* 1.3 57.2 + - + +
205A ALA* 3.4 3.6 + - + +
206A GLY 2.8 28.4 + - - -
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Residues in contact with GLU 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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115A PHE* 3.5 24.4 - - + -
201A SER* 3.0 19.6 + - - +
202A PRO* 1.3 77.1 - - + +
204A GLU* 1.3 65.3 + - - +
206A GLY* 3.1 1.2 + - - -
207A ARG* 2.8 40.5 + - - +
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Residues in contact with GLU 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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170A LEU* 5.3 0.2 - - - +
198A LEU 5.0 1.6 - - - +
199A ALA* 3.8 17.0 - - + -
200A TRP* 3.7 31.5 - - + +
201A SER* 3.1 21.6 + - - +
203A GLU* 1.3 78.5 - - - +
205A ALA* 1.3 62.5 + - - +
207A ARG* 2.6 42.6 + - - +
208A TYR* 3.1 25.8 + - - +
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Residues in contact with ALA 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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112A VAL* 4.2 5.2 - - + -
140A PHE* 4.1 11.2 - - + -
170A LEU* 3.7 24.6 - - + +
172A GLN* 4.0 13.0 - - + +
199A ALA* 3.9 8.9 - - + +
201A SER 3.2 9.9 + - - +
202A PRO* 3.4 10.1 - - + +
203A GLU 3.2 0.2 - - - -
204A GLU* 1.3 80.9 - - - +
206A GLY* 1.3 57.3 + - - +
208A TYR* 3.3 2.8 + - - +
209A LEU* 3.0 35.5 + - - +
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Residues in contact with GLY 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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112A VAL* 3.5 20.1 - - - +
115A PHE* 4.5 5.6 - - - -
116A VAL* 3.9 10.3 - - - -
202A PRO 2.8 15.9 + - - -
203A GLU 3.6 2.0 - - - -
205A ALA* 1.3 71.1 - - - +
207A ARG* 1.3 60.1 + - - +
209A LEU* 3.2 3.0 + - - +
210A GLU* 2.9 40.3 + - - +
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Residues in contact with ARG 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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115A PHE* 5.4 0.6 - - - -
203A GLU* 2.8 26.1 + - - +
204A GLU* 2.6 46.8 + - - +
206A GLY* 1.3 74.1 - - - +
208A TYR* 1.3 57.3 + - + +
210A GLU* 3.9 10.7 + - - +
211A THR* 2.9 34.4 + - - +
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Residues in contact with TYR 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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138A ALA* 5.8 2.5 - - + -
168A VAL* 3.5 18.9 - - + +
170A LEU* 4.3 14.6 - - + -
197A ILE* 3.4 54.5 - - + +
204A GLU 3.1 19.8 + - - +
205A ALA* 3.6 4.5 - - - +
206A GLY 3.2 0.2 - - - -
207A ARG* 1.3 75.7 - - + +
209A LEU* 1.3 67.4 + - + +
211A THR* 3.4 11.7 - - + +
212A TYR* 2.8 64.3 + + + +
219A PRO* 3.7 12.2 - - + +
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Residues in contact with LEU 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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101A ILE* 4.2 13.8 - - + +
112A VAL* 4.0 16.2 - - + -
113A LEU* 5.8 0.2 - - + -
116A VAL* 5.0 5.6 - - + -
130A TYR* 3.5 57.4 - - + -
132A LEU* 4.6 7.4 - - + +
138A ALA* 4.0 17.0 - - + -
170A LEU* 4.0 16.2 - - + -
205A ALA* 3.0 23.5 + - + +
206A GLY* 3.6 3.6 - - - +
208A TYR* 1.3 79.0 - - + +
210A GLU* 1.3 65.3 + - + +
212A TYR* 3.3 5.1 + - + +
213A LYS* 3.0 27.5 + - - +
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Residues in contact with GLU 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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101A ILE* 5.1 0.4 - - + -
115A PHE* 5.7 1.4 - - - -
116A VAL* 3.9 24.0 - - + -
117A ARG* 2.7 40.0 + - - -
118A ASN* 2.6 47.0 + - + +
119A VAL* 3.1 20.2 - - + +
206A GLY* 2.9 24.4 + - - +
207A ARG* 3.9 8.0 + - - +
209A LEU* 1.3 76.5 - - + +
211A THR* 1.3 56.8 + - - +
214A ALA* 2.9 27.8 + - - +
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Residues in contact with THR 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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118A ASN* 5.4 1.6 - - - -
207A ARG 2.9 25.9 + - - +
208A TYR* 3.4 17.0 - - + +
210A GLU* 1.3 77.2 - - - +
212A TYR* 1.3 65.4 + - - +
214A ALA* 4.2 5.4 - - - -
215A TYR* 3.0 50.1 + - - +
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Residues in contact with TYR 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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132A LEU* 3.8 27.6 - - + -
136A THR* 3.4 33.8 - - + +
138A ALA* 6.1 0.4 - - + -
166A LEU* 3.5 8.1 - - - +
168A VAL* 4.1 8.3 - - + -
208A TYR* 2.8 52.5 + + + +
209A LEU* 3.7 5.8 - - + +
210A GLU 3.2 0.2 - - - -
211A THR* 1.3 79.5 - - - +
213A LYS* 1.3 51.7 + - - +
215A TYR* 5.1 0.7 - - - -
216A GLU* 2.7 38.9 + - - -
217A GLN 3.2 26.8 + - - -
218A LYS* 3.8 4.9 - - - -
219A PRO* 3.2 33.3 - - + +
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Residues in contact with LYS 213 (chain A).
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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98A SER* 2.8 25.9 + - - -
99A ASN* 3.4 23.1 - - - +
100A SER 4.1 2.5 - - - +
101A ILE* 3.7 15.9 - - + -
119A VAL* 3.7 22.7 - - + -
132A LEU* 2.7 46.9 + - + +
209A LEU 3.0 15.7 + - - +
212A TYR* 1.3 78.4 - - - +
214A ALA* 1.3 67.1 + - - +
216A GLU* 2.7 44.4 + - + +
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Residues in contact with ALA 214 (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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118A ASN* 4.5 9.2 - - - +
119A VAL* 3.9 12.7 - - + +
210A GLU 2.9 20.3 + - - +
211A THR* 3.9 7.2 - - - +
213A LYS* 1.3 78.4 - - - +
215A TYR* 1.3 70.3 + - + +
216A GLU* 4.9 1.0 - - - +
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Residues in contact with TYR 215 (chain A).
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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211A THR* 3.0 41.5 + - - +
212A TYR* 4.1 1.1 - - - +
214A ALA* 1.3 91.0 - - + +
216A GLU* 1.3 68.6 + - - +
217A GLN* 3.1 24.5 + - + +
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Residues in contact with GLU 216 (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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97A LYS* 5.1 8.4 + - - -
98A SER 3.8 5.2 - - - +
132A LEU* 4.3 2.5 - - + +
212A TYR* 2.7 23.2 + - - -
213A LYS* 2.7 49.9 + - + +
214A ALA 4.8 1.1 - - - +
215A TYR* 1.3 75.7 - - - +
217A GLN* 1.3 62.2 + - - +
218A LYS* 3.7 5.7 + - - -
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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