Contacts of the strand formed by residues 211 - 219 (chain A) in PDB entry 5JPM
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 GLY 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A SER* 4.1 9.9 - - - -
209A GLU 3.6 1.6 + - - -
210A PRO* 1.3 75.9 - - - +
212A THR* 1.3 63.9 + - - -
213A TRP 4.0 0.2 - - - -
232A GLU* 3.4 6.7 - - - +
233A VAL* 2.9 36.0 + - - +
234A LYS* 4.8 5.7 - - - +
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Residues in contact with THR 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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180A ASN 3.8 2.1 - - - +
181A SER* 3.3 22.3 + - - +
211A GLY* 1.3 71.2 - - - -
213A TRP* 1.3 67.0 + - - +
214A LYS* 5.3 0.9 - - - +
230A GLN* 5.0 18.5 + - - +
231A PHE 3.4 7.6 - - - +
232A GLU* 3.6 33.7 - - + +
614A LYS* 5.5 4.7 - - - +
616A HIS* 5.2 2.9 - - + -
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Residues in contact with TRP 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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178A VAL* 4.3 12.6 - - + -
179A GLU 3.5 5.4 - - - +
180A ASN* 3.4 24.0 - - + +
181A SER* 3.3 27.9 + - - +
186A VAL* 4.2 17.7 - - + -
202A PHE* 4.2 15.9 - + - -
204A ILE* 4.0 19.1 - - + -
205A PRO* 4.1 8.7 - - + -
208A SER* 3.9 15.3 - - - -
209A GLU 4.4 5.1 + - - -
211A GLY 4.0 0.4 + - - -
212A THR* 1.3 75.3 - - - +
214A LYS* 1.3 61.1 + - - +
230A GLN* 3.2 7.6 - - - +
231A PHE* 2.9 63.6 + + + +
233A VAL* 3.5 26.1 - - + +
1054B MET* 5.3 0.9 - - + -
1058B GLN* 3.7 28.5 - - - -
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Residues in contact with LYS 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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177A MET 4.1 0.3 - - - +
178A VAL* 3.6 1.4 - - - -
179A GLU* 2.9 70.1 + - + +
180A ASN 4.6 0.6 + - - +
212A THR 4.3 0.9 + - - +
213A TRP* 1.3 76.2 - - - +
215A ILE* 1.3 65.0 + - - +
216A SER* 4.9 4.5 - - - +
228A SER* 3.9 27.1 - - - +
229A THR 3.7 10.8 - - - +
230A GLN* 4.1 21.9 + - + +
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Residues in contact with ILE 215 (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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143A LEU* 3.3 18.2 - - + +
145A THR* 3.9 22.7 - - + -
156A VAL* 5.1 0.4 - - + -
158A TYR* 3.8 36.1 - - + -
176A VAL* 4.0 16.6 - - + -
177A MET 3.5 9.6 - - - +
178A VAL* 3.8 26.9 - - + -
202A PHE* 4.3 5.4 - - + -
214A LYS* 1.3 75.5 - - - +
216A SER* 1.3 62.9 + - - +
228A SER* 3.1 3.8 - - - -
229A THR* 2.8 39.1 + - + +
231A PHE* 4.0 17.0 - - + -
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Residues in contact with SER 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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143A LEU* 4.6 1.1 - - - -
175A THR 4.0 1.2 - - - +
176A VAL* 3.5 2.2 - - - -
177A MET* 2.8 65.5 + - - +
179A GLU* 5.1 3.7 + - - +
214A LYS* 4.1 7.2 + - - -
215A ILE* 1.3 74.3 - - - +
217A ALA* 1.3 57.7 + - - +
218A ARG* 6.1 0.2 - - - -
226A ASN* 5.1 11.2 - - - -
227A SER 3.6 6.5 - - - -
228A SER* 3.9 13.0 - - - -
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Residues in contact with ALA 217 (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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141A LEU* 3.4 11.1 - - + +
143A LEU* 4.2 9.8 - - + +
160A VAL* 3.9 27.8 - - + -
174A ILE* 4.6 6.1 - - + -
175A THR 3.6 5.2 - - - +
176A VAL* 4.3 17.7 - - + -
216A SER* 1.3 74.4 - - - +
218A ARG* 1.3 60.8 + - - +
226A ASN* 4.4 0.7 - - - -
227A SER* 2.8 34.8 + - - +
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Residues in contact with ARG 218 (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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141A LEU* 3.6 9.4 - - - -
174A ILE* 3.3 4.2 - - - +
175A THR* 2.7 61.2 + - - +
216A SER 6.1 0.2 - - - -
217A ALA* 1.3 76.9 - - - +
219A PHE* 1.3 78.8 + - - +
220A SER* 3.1 19.4 + - - +
222A GLY 3.3 11.6 + - - +
223A LEU* 3.5 41.2 + - - +
225A SER 3.9 3.1 - - - +
226A ASN* 3.7 25.4 - - + +
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Residues in contact with PHE 219 (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 ARG* 3.3 52.3 - - + +
139A GLY* 4.1 7.4 - - - -
141A LEU* 3.8 27.1 - - + -
162A ALA* 4.3 10.1 - - + -
163A LEU 4.1 14.8 - - - -
164A ASP* 6.0 0.2 - - - -
170A SER* 4.0 11.9 - - - -
172A ASP* 3.8 30.5 - - + -
173A THR 3.6 3.6 - - - +
174A ILE* 3.6 22.0 - - + +
218A ARG* 1.3 88.5 + - - +
220A SER* 1.3 65.4 + - - +
221A ASP* 4.4 1.1 - - - +
222A GLY* 3.0 20.0 + - - +
225A SER* 3.5 13.9 + - - +
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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