Contacts of the helix formed by residues 251 - 267 (chain H) in PDB entry 5LN3
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 251 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H VAL* 1.3 72.1 - - - +
252H GLU* 1.3 63.9 + - - +
253H GLY* 3.2 4.2 - - - +
254H ALA* 3.2 14.4 + - - +
255H ARG* 3.2 24.3 + - - +
258H ARG* 5.8 0.5 + - - -
297H ARG* 4.7 7.3 - - - +
254M PRO 5.6 0.2 - - - -
257M VAL* 4.6 16.2 - - - +
258M GLN* 4.3 4.9 - - - -
259M MET 4.3 10.8 - - - -
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Residues in contact with GLU 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H GLN* 3.9 30.9 + - + +
249H TYR* 3.1 28.7 - - + +
250H VAL 3.1 4.4 + - - +
251H GLY* 1.3 75.7 - - - +
253H GLY* 1.3 57.3 + - - +
255H ARG* 3.2 29.8 + - - +
256H MET* 3.1 39.0 + - + +
259M MET* 3.4 28.2 - - + +
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Residues in contact with GLY 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H LEU* 4.4 11.2 - - - +
246H VAL* 6.1 0.2 - - - -
247H GLN* 4.9 5.5 - - - +
249H TYR 4.5 1.8 + - - -
250H VAL* 5.4 0.2 - - - +
251H GLY 3.2 3.2 - - - +
252H GLU* 1.3 79.2 - - - +
254H ALA* 1.4 61.4 + - - +
256H MET* 3.2 19.2 + - - +
257H VAL* 3.4 18.7 + - - +
298H THR* 4.2 16.2 - - - +
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Residues in contact with ALA 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H GLY* 3.2 14.4 + - - +
253H GLY* 1.4 74.3 - - - +
255H ARG* 1.3 63.4 + - - +
257H VAL* 3.1 7.5 + - - +
258H ARG* 3.1 34.2 + - - +
297H ARG* 5.3 7.9 - - + +
298H THR* 5.1 3.4 + - - +
301H GLU* 4.1 28.7 - - + +
254M PRO* 4.5 20.4 - - + +
255M GLN* 6.1 0.2 - - - -
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Residues in contact with ARG 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H GLN* 4.3 14.3 - - - +
144H ARG* 3.8 30.6 - - - +
251H GLY 3.2 10.7 + - - +
252H GLU* 3.2 40.0 + - - +
254H ALA* 1.3 76.3 - - - +
256H MET* 1.4 67.4 + - - +
258H ARG* 3.3 20.5 - - - +
259H GLU* 3.1 41.3 + - + +
173M LYS* 5.9 5.1 - - - +
258M GLN* 4.0 19.8 + - - +
259M MET* 5.3 2.2 - - - +
260M PHE* 4.4 12.7 - - - -
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Residues in contact with MET 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H LEU* 4.0 43.8 - - + +
247H GLN* 4.0 26.9 - - + -
252H GLU* 3.1 31.8 + - + +
253H GLY* 3.5 7.9 - - - +
254H ALA 3.2 0.4 - - - -
255H ARG* 1.4 80.5 - - - +
257H VAL* 1.4 65.5 + - + +
259H GLU* 3.1 28.0 + - - +
260H LEU* 3.1 15.4 + - - +
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Residues in contact with VAL 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H LEU* 5.2 11.7 - - + -
253H GLY 3.4 15.3 - - - +
254H ALA* 3.1 8.4 + - - +
256H MET* 1.4 73.0 - - + +
258H ARG* 1.4 65.6 + - - +
260H LEU* 3.3 10.6 - - - +
261H PHE* 3.3 21.5 + - + +
280H ILE* 5.9 0.7 - - + -
298H THR* 3.6 28.5 - - + +
301H GLU* 3.9 18.8 - - + -
302H LEU* 3.9 35.4 - - + -
305H GLN* 4.5 9.0 - - + -
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Residues in contact with ARG 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H ARG* 3.5 24.2 - - - +
156H LYS* 3.3 31.4 - - - +
251H GLY 5.8 0.4 + - - -
254H ALA* 3.1 25.4 + - - +
255H ARG* 3.3 17.5 - - + +
257H VAL* 1.4 61.3 - - - +
259H GLU* 1.4 60.5 + - - +
261H PHE* 3.1 14.1 + - - +
262H GLU* 3.1 26.4 + - - +
301H GLU* 4.1 9.9 - - - +
305H GLN* 4.0 25.3 + - - +
173M LYS* 4.4 7.5 + - - +
174M ALA* 3.7 12.5 - - - +
255M GLN* 3.2 42.4 + - - +
258M GLN* 5.2 6.9 - - - +
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Residues in contact with GLU 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H GLN* 4.3 16.6 - - - +
144H ARG* 5.1 2.7 - - - +
158H ASP 4.3 1.9 - - - +
159H PRO 5.0 2.6 - - - +
160H THR* 4.2 11.1 - - + +
161H VAL* 2.8 36.2 - - - +
162H THR* 4.6 9.6 - - + +
255H ARG* 3.1 42.7 + - + +
256H MET* 3.1 22.2 + - - +
258H ARG* 1.4 75.3 - - - +
260H LEU* 1.3 62.6 + - - +
262H GLU* 3.4 16.5 + - - +
263H MET* 3.3 23.6 + - - +
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Residues in contact with LEU 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H THR* 6.1 0.2 - - - -
164H MET* 6.5 0.2 - - + -
238H ILE* 4.8 2.7 - - + -
240H VAL* 3.9 28.9 - - + -
245H LEU* 6.2 4.9 - - + -
256H MET 3.1 9.8 + - - +
257H VAL* 3.3 13.2 - - - +
259H GLU* 1.3 79.7 - - - +
261H PHE* 1.4 73.4 + - + +
263H MET* 3.4 24.3 + - + +
264H ALA* 3.0 25.8 + - + +
272H ILE* 4.3 38.8 - - + -
274H PHE* 4.6 12.3 - - + -
302H LEU* 6.0 2.9 - - + -
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Residues in contact with PHE 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H ILE* 4.7 2.4 - - + +
210H LYS* 4.2 15.7 - - - -
257H VAL* 3.3 8.0 + - + +
258H ARG 3.1 8.8 + - - +
260H LEU* 1.4 93.4 - - + +
262H GLU* 1.4 56.3 + - + +
264H ALA* 3.1 10.7 + - + +
265H ARG* 3.1 34.8 + - - +
272H ILE* 6.6 0.2 - - + -
274H PHE* 6.5 0.7 - + - -
302H LEU* 5.6 9.2 - - + -
305H GLN* 3.3 59.0 - - + +
306H LEU* 4.1 27.6 - - + -
310H ASP* 3.8 19.5 - - + -
311H PRO 5.3 1.1 - - - -
315H ILE* 5.3 9.6 - - + +
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Residues in contact with GLU 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LEU 5.6 0.2 - - - +
94H GLN* 5.3 1.2 - - - +
144H ARG* 3.7 19.5 + - - -
155H PRO 4.1 7.3 - - - +
156H LYS* 3.4 30.9 - - + +
157H ILE* 3.2 36.5 + - + +
158H ASP* 3.3 18.0 + - - +
160H THR* 4.4 10.2 - - - +
258H ARG* 3.1 28.9 + - - +
259H GLU* 3.5 13.4 + - - +
261H PHE* 1.4 72.1 - - + +
263H MET* 1.3 61.4 + - - +
266H THR* 2.8 23.9 + - - -
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Residues in contact with MET 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H ASP 3.3 7.6 + - - -
159H PRO* 3.9 21.3 - - + +
162H THR* 3.7 31.4 - - + -
164H MET* 4.3 20.4 - - + -
166H VAL* 5.7 4.3 - - + -
238H ILE* 5.3 19.1 - - + -
259H GLU 3.3 6.4 + - - +
260H LEU* 3.5 27.1 - - + +
262H GLU* 1.3 79.4 - - - +
264H ALA* 1.3 63.7 + - - +
266H THR* 3.3 9.6 + - - -
267H LYS* 3.3 45.1 - - + +
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Residues in contact with ALA 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H ILE* 6.0 2.5 - - - -
260H LEU* 3.0 16.7 + - + +
261H PHE* 3.1 15.7 + - + +
263H MET* 1.3 79.4 - - - +
265H ARG* 1.3 59.6 + - - +
266H THR 3.5 0.2 + - - -
267H LYS* 3.8 1.1 + - - +
268H LYS 3.6 23.9 + - - +
270H CYS* 4.0 17.6 - - - -
272H ILE* 4.6 10.5 - - + -
315H ILE* 3.7 27.5 - - + +
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Residues in contact with ARG 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H ILE* 3.6 37.7 - - + +
261H PHE* 3.1 14.6 + - + +
262H GLU 3.6 0.2 + - - -
264H ALA* 1.3 78.5 - - - +
266H THR* 1.4 61.8 + - - +
268H LYS* 3.5 27.0 + - - +
310H ASP* 3.2 41.3 + - - +
311H PRO* 4.2 5.5 + - - +
312H ARG 4.2 2.9 + - - +
313H GLY* 3.6 35.7 - - - +
314H ASN 5.0 0.4 - - - +
315H ILE* 4.1 16.3 - - - +
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Residues in contact with THR 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H ILE* 3.1 27.9 + - + +
158H ASP* 3.6 3.5 + - - -
159H PRO* 4.4 7.0 - - + -
262H GLU 2.8 17.7 + - - -
263H MET* 3.3 3.0 + - - -
265H ARG* 1.4 76.1 - - - +
267H LYS* 1.3 84.4 + - + +
268H LYS* 3.3 24.7 + - - +
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Residues in contact with LYS 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H PRO* 3.4 37.1 - - - +
236H CYS* 5.4 8.1 - - - -
238H ILE* 5.9 4.3 - - + -
263H MET* 3.3 27.0 + - + +
264H ALA* 4.2 4.3 - - - +
265H ARG 3.4 0.2 - - - -
266H THR* 1.3 102.2 - - + +
268H LYS* 1.3 64.2 + - - +
269H ALA* 3.0 19.2 + - - +
270H CYS* 5.1 10.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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