Contacts of the helix formed by residues 245 - 260 (chain A) in PDB entry 6RZ5
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 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ALA* 2.9 19.9 + - - -
244A VAL* 1.3 75.9 - - - +
246A PHE* 1.3 66.3 + - - +
247A MET 3.6 0.2 - - - -
248A PRO* 3.8 5.0 - - - +
249A TYR 4.3 4.5 + - - -
283A LEU* 2.7 26.1 + - - +
284A ALA* 3.1 34.6 + - - +
286A SER* 4.6 0.2 - - - -
287A ASN* 3.3 17.1 + - - +
290A PHE* 4.2 18.8 - - - -
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Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.7 26.5 - - + -
110A SER* 4.3 11.0 - - - -
111A ILE* 3.6 37.0 - - + -
114A MET* 3.8 31.2 - - + -
198A PHE* 3.8 15.9 - - + -
241A ALA* 3.3 22.8 + - + -
242A PHE* 3.7 27.6 - + - +
245A SER* 1.3 74.7 - - - +
247A MET* 1.4 63.2 + - - +
249A TYR* 3.8 3.4 + - - +
250A HIS* 2.8 32.0 + - - +
287A ASN* 3.6 30.5 - - + -
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Residues in contact with MET 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 3.6 22.6 - - + -
202A PHE* 3.2 34.3 - - + -
242A PHE 2.9 24.5 + - - +
243A LEU* 3.6 29.4 - - + +
246A PHE* 1.4 71.7 - - - +
248A PRO* 1.4 70.5 - - + +
250A HIS* 3.3 3.3 + - - +
251A ILE* 3.1 43.8 + - + +
2019A OLA 3.8 28.7 - - + -
2016B OLA 4.4 6.7 - - + -
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Residues in contact with PRO 248 (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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243A LEU 3.2 20.4 - - - +
244A VAL* 3.4 23.3 - - - +
245A SER 3.8 6.3 - - - +
247A MET* 1.4 85.5 - - + +
249A TYR* 1.4 50.3 + - - +
251A ILE* 3.3 9.1 + - + +
252A GLN* 2.9 36.9 + - - +
280A THR* 3.8 20.4 - - + +
283A LEU* 4.2 14.4 - - + -
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Residues in contact with TYR 249 (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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104A TYR* 3.2 14.0 - + - -
107A LEU* 3.6 26.0 - - + -
108A TYR* 3.9 4.9 - - - -
245A SER 4.3 2.3 + - - +
246A PHE 3.8 6.2 + - - +
247A MET 3.3 0.6 - - - -
248A PRO* 1.4 77.3 - - - +
250A HIS* 1.3 74.4 + + - +
252A GLN* 3.4 1.7 + - - +
253A ARG* 2.9 69.3 + - - +
280A THR* 3.7 25.2 - - - +
281A LEU* 4.3 13.7 - - + -
284A ALA* 3.9 10.8 - - + -
2001A ZLK 2.7 63.5 + + - -
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Residues in contact with HIS 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.5 2.5 - - + -
108A TYR* 2.8 40.6 + + - -
111A ILE* 4.2 12.8 - - + -
190A HIS* 4.3 0.3 - - - -
193A SER 5.0 0.2 + - - -
194A LEU* 3.7 29.0 - - + +
198A PHE* 3.6 40.0 - + + +
246A PHE* 2.8 25.0 + - + +
247A MET 3.3 4.1 + - - +
249A TYR* 1.3 89.0 - + - +
251A ILE* 1.4 62.5 + - + +
253A ARG* 4.0 19.1 + - - +
254A THR* 3.0 25.1 + - - -
2016B OLA 4.7 1.5 - - + +
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Residues in contact with ILE 251 (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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247A MET* 3.1 40.8 + - + +
248A PRO* 3.8 6.5 - - + +
250A HIS* 1.4 74.2 - - - +
252A GLN* 1.3 63.3 + - - +
254A THR* 3.3 7.5 + - - -
255A ILE* 3.1 40.3 + - + +
2019A OLA 4.3 35.7 - - + +
2016B OLA 3.8 43.9 - - + +
2017B OLA 5.6 1.6 - - + -
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Residues in contact with GLN 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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248A PRO 2.9 18.2 + - - +
249A TYR 3.8 2.0 - - - +
251A ILE* 1.3 78.0 - - - +
253A ARG* 1.4 50.9 + - - +
255A ILE* 3.4 15.9 + - - +
256A HIS* 2.7 44.1 + - - +
273A MET* 3.9 34.3 + - - +
276A SER* 3.6 31.2 + - - +
277A VAL 4.5 0.4 - - - +
280A THR* 3.5 32.4 - - + +
2001A ZLK 4.1 9.2 - - + -
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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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108A TYR* 2.9 24.1 + - - -
190A HIS* 2.9 45.7 + - + +
193A SER* 3.0 21.6 + - - -
194A LEU* 3.7 7.9 - - - +
249A TYR* 2.9 49.1 + - + +
250A HIS* 4.2 11.5 - - - +
252A GLN* 1.4 71.0 - - - +
254A THR* 1.4 64.0 + - - +
256A HIS* 4.4 0.9 - - - -
257A LEU* 3.1 33.3 + - + +
2001A ZLK 3.5 65.6 + - + -
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Residues in contact with THR 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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190A HIS* 2.9 25.4 + - - +
191A TYR* 3.6 24.7 - - + +
194A LEU* 3.8 9.2 - - - +
250A HIS 3.0 14.9 + - - -
251A ILE 3.3 9.0 + - - -
253A ARG* 1.4 77.6 - - - +
255A ILE* 1.4 62.8 + - - +
257A LEU* 4.1 0.7 - - - +
258A HIS* 3.3 32.7 + - + -
2007A OLC 4.0 22.7 - - + +
2016B OLA 4.0 15.5 - - + +
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Residues in contact with ILE 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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251A ILE* 3.1 35.6 + - + +
252A GLN* 3.7 17.7 - - - +
254A THR* 1.4 75.6 - - - +
256A HIS* 1.4 55.7 + - - +
258A HIS* 3.4 4.7 + - - +
259A PHE* 3.0 28.8 + - + +
273A MET* 3.8 29.6 - - + -
2007A OLC 5.5 4.5 - - - +
2019A OLA 5.2 5.8 - - - +
2016B OLA 4.2 28.7 - - + -
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Residues in contact with HIS 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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176A PRO* 4.5 1.5 - - + +
177A PRO* 2.8 37.3 + - + +
178A GLN 4.8 1.8 - - - -
252A GLN* 2.7 25.9 + - - +
253A ARG 4.0 2.9 - - - +
255A ILE* 1.4 72.7 - - - +
257A LEU* 1.3 65.1 + - + +
259A PHE* 3.2 13.8 + + - +
260A LEU* 3.2 31.6 + - + +
273A MET* 4.3 22.2 + - + +
274A GLN* 3.9 17.7 - - - -
277A VAL* 3.5 27.4 - - + +
2001A ZLK 3.7 28.7 - - + +
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Residues in contact with LEU 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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177A PRO* 4.3 25.6 - - + -
186A VAL* 4.4 20.2 - - + +
187A LEU* 3.8 17.9 - - + -
190A HIS* 3.5 39.5 - - + +
253A ARG* 3.1 21.5 + - + +
254A THR* 4.2 1.8 - - - +
256A HIS* 1.3 83.8 - - + +
258A HIS* 1.4 59.0 + - - +
260A LEU* 3.5 11.2 - - + +
261A HIS* 3.1 26.0 + - - +
2001A ZLK 4.2 24.2 - - + -
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Residues in contact with HIS 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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187A LEU* 3.8 29.5 - - + +
191A TYR* 2.7 32.9 + + - -
254A THR* 3.3 28.6 + - + +
255A ILE* 3.9 3.4 - - - +
257A LEU* 1.4 71.9 - - - +
259A PHE* 1.4 63.9 + - - +
260A LEU 3.2 2.2 - - - -
261A HIS* 3.1 16.2 + - - +
262A ASN* 3.5 4.3 + - - +
2007A OLC 3.4 63.4 + - + +
2009B OLC 3.6 30.6 + - - -
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Residues in contact with PHE 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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178A GLN 5.3 2.9 - - - -
255A ILE* 3.0 15.9 + - + +
256A HIS* 3.2 14.6 + + - +
258A HIS* 1.4 75.0 - - - +
260A LEU* 1.3 72.8 + - + +
262A ASN* 3.3 23.8 + - + +
264A THR 5.4 3.1 - - - -
265A LYS* 3.4 27.2 - - + +
266A PRO* 5.6 0.9 - - + -
269A SER* 3.1 32.8 - - - -
270A VAL* 3.8 23.8 - - + -
273A MET* 3.9 39.5 - - + -
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Residues in contact with LEU 260 (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 PRO* 3.3 35.2 - - + +
178A GLN 3.7 10.1 - - - +
179A ASP* 3.8 4.0 - - - +
180A ASN* 3.7 10.2 - - - +
181A GLN 3.5 39.3 - - - +
182A THR* 3.5 26.2 - - - +
256A HIS* 3.2 31.2 + - + +
257A LEU* 3.5 15.3 - - + +
258A HIS 3.2 0.4 - - - -
259A PHE* 1.3 88.6 - - + +
261A HIS* 1.3 56.4 + - - +
262A ASN 3.4 0.2 - - - -
265A LYS* 3.3 23.1 + - - +
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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