Contacts of the helix formed by residues 251 - 259 (chain A) in PDB entry 5JLH
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 ASN 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A GLU* 5.2 0.3 - - - +
195A ARG* 3.7 13.5 + - - +
226A MET* 4.4 15.2 - - + +
229A ALA* 3.6 29.5 - - + +
235A LEU* 4.9 0.4 - - - +
250A GLY* 1.4 66.9 - - - -
252A GLU* 1.3 81.8 + - - +
253A ARG 3.0 3.5 + - - -
254A PHE* 3.1 36.6 + - + -
255A ARG* 3.4 40.1 + - - +
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Residues in contact with GLU 252 (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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188A LEU* 4.2 4.7 - - + +
191A ILE* 3.5 34.4 - - + +
192A LEU* 2.9 43.8 - - + +
194A GLU* 4.8 5.9 - - - +
195A ARG* 3.1 29.5 + - - +
249A ILE* 3.2 24.7 - - + +
250A GLY 4.7 2.0 - - - +
251A ASN* 1.3 87.7 + - - +
253A ARG* 1.3 64.5 + - - +
255A ARG* 3.9 14.7 - - - +
256A CYS* 3.7 15.4 + - - +
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Residues in contact with ARG 253 (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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188A LEU* 5.5 1.6 - - - -
215A LEU* 2.7 33.2 + - - +
216A CYS* 3.5 18.5 - - - +
217A TYR* 3.3 37.2 - - - +
234A SER 3.6 7.9 + - - -
235A LEU 3.0 29.4 + - - -
236A GLU 3.6 0.2 - - - -
237A LYS* 3.1 60.4 - - - +
249A ILE* 4.2 22.4 + - + +
250A GLY 3.1 15.5 + - - +
251A ASN 3.0 0.4 - - - -
252A GLU* 1.3 84.6 - - - +
254A PHE* 1.3 61.6 + - + +
256A CYS* 3.4 11.1 + - - +
257A PRO* 3.4 9.5 - - - +
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Residues in contact with PHE 254 (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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217A TYR* 3.2 57.9 - + + +
218A VAL* 4.8 1.9 - - - -
219A ALA* 4.3 8.6 + - + +
222A PHE* 3.9 31.4 - + - -
225A GLU* 3.6 21.3 - - + +
226A MET* 3.5 36.6 - - + -
235A LEU* 4.7 9.2 - - + -
250A GLY 4.5 3.8 - - - -
251A ASN* 3.1 32.6 + - + -
253A ARG* 1.3 75.2 - - - +
255A ARG* 1.3 70.1 + - + +
256A CYS 3.0 2.9 + - - -
257A PRO* 3.2 10.7 - - - +
258A GLU* 3.4 10.4 + - - +
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Residues in contact with ARG 255 (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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187A TYR* 4.0 22.5 + - + +
191A ILE* 3.8 20.8 - - + +
194A GLU* 2.4 36.8 + - - -
222A PHE* 3.6 27.1 - - + -
226A MET* 4.5 12.5 - - - -
251A ASN* 3.4 36.3 + - - +
252A GLU* 3.9 14.0 - - - +
254A PHE* 1.3 80.7 - - + +
256A CYS* 1.3 66.3 + - - +
257A PRO 3.5 0.2 - - - -
258A GLU* 3.2 20.2 + - + +
259A ALA 3.6 2.9 + - - -
265A PHE* 4.5 8.2 - - + -
112D LYS* 5.6 4.4 - - - +
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Residues in contact with CYS 256 (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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184A LEU* 3.3 56.5 - - - +
187A TYR* 4.1 13.2 - - + -
188A LEU* 3.5 35.4 - - + -
212A LYS* 4.4 11.7 - - - -
216A CYS* 4.1 2.2 - - - -
252A GLU 3.7 1.7 + - - +
253A ARG 3.4 7.2 + - - +
254A PHE 3.0 1.6 - - - -
255A ARG* 1.3 83.0 - - - +
257A PRO* 1.3 72.4 - - + +
258A GLU 3.3 0.2 + - - -
259A ALA* 3.3 7.1 + - - +
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Residues in contact with PRO 257 (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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184A LEU* 4.5 5.4 - - + -
216A CYS* 3.8 17.9 - - + -
217A TYR 3.6 17.3 - - - +
218A VAL* 3.4 24.0 - - + -
253A ARG 3.4 9.4 - - - +
254A PHE 3.2 9.0 - - - +
256A CYS* 1.3 92.9 - - + +
258A GLU* 1.3 60.7 + - - +
259A ALA 2.9 7.3 + - - -
260A LEU* 3.0 21.8 + - + +
261A PHE* 3.8 7.1 - - - -
305A TYR* 3.7 28.3 - - + -
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Residues in contact with GLU 258 (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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218A VAL* 4.5 6.0 - - - +
219A ALA* 4.8 3.3 + - - +
222A PHE* 3.5 40.4 - - + +
254A PHE 3.4 6.4 + - - +
255A ARG* 3.2 25.5 + - - +
256A CYS 3.2 0.6 - - - -
257A PRO* 1.3 78.3 - - - +
259A ALA* 1.3 62.2 + - - +
261A PHE* 2.8 19.4 + - - +
262A GLN* 3.1 24.8 + - + +
265A PHE* 3.6 19.1 - - + -
311A ARG* 3.1 42.0 + - - -
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Residues in contact with ALA 259 (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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179A LEU* 4.4 2.9 - - - +
184A LEU* 3.6 15.0 - - + -
187A TYR* 4.9 6.5 - - + -
255A ARG 3.6 3.6 + - - +
256A CYS 3.3 15.1 + - - +
257A PRO 2.9 0.6 - - - -
258A GLU* 1.3 78.9 - - - +
260A LEU* 1.3 63.7 + - + +
262A GLN 2.9 29.7 + - - +
263A PRO* 3.3 8.7 - - - +
265A PHE* 4.5 9.8 - - + -
266A LEU* 4.2 23.6 - - + -
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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