Contacts of the helix formed by residues 288 - 301 (chain M) in PDB entry 6D6R
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 288 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286M ILE* 3.8 12.8 - - - +
287M PRO* 1.3 77.7 - - + +
289M ALA* 1.3 65.3 + - - +
290M ARG* 3.0 5.6 + - - -
291M GLN* 3.0 24.7 + - + +
292M PHE* 3.3 9.7 + - - +
558M PRO* 4.1 10.9 - - + +
559M LEU* 2.9 57.1 + - - +
589M PHE* 4.4 10.0 - - - -
593M GLN* 5.1 4.0 - - - +
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Residues in contact with ALA 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158M LEU* 3.7 26.0 - - + +
160M SER* 5.2 5.8 - - - -
286M ILE* 3.8 19.6 + - + +
287M PRO 3.2 4.7 - - - +
288M ASN* 1.3 79.8 + - - +
290M ARG* 1.3 63.6 + - + +
292M PHE* 3.1 7.5 + - - +
293M ALA* 2.9 23.8 + - - +
306M VAL* 3.8 19.1 - - + -
308M TYR* 5.9 4.0 - - + -
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Residues in contact with ARG 290 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101M VAL* 3.1 45.2 - - + +
102M GLN 5.4 0.8 + - - -
113M GLU* 2.3 49.6 + - + +
287M PRO 5.4 6.1 - - - +
288M ASN* 3.0 1.7 + - - -
289M ALA* 1.3 79.0 - - + +
291M GLN* 1.3 66.8 + - + +
293M ALA* 3.3 6.9 + - - +
294M GLU* 2.9 37.8 + - - +
306M VAL* 5.3 6.7 - - + -
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Residues in contact with GLN 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288M ASN* 3.0 21.6 + - + +
290M ARG* 1.3 79.6 - - + +
292M PHE* 1.3 63.7 + - - +
294M GLU* 3.3 12.7 + - - +
295M TRP* 2.9 19.9 + - - +
589M PHE* 4.5 13.7 - - + -
592M PHE* 3.1 35.2 - - + +
593M GLN* 5.4 6.5 - - + -
596M ARG* 3.4 43.7 + - - +
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Residues in contact with PHE 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158M LEU* 3.8 21.3 - - + -
254M ILE* 5.0 9.9 - - + -
257M MET* 4.4 16.4 - - + -
270M ILE* 4.7 5.2 - - + -
281M PHE* 3.5 55.9 - + - -
286M ILE* 5.6 3.1 - - + -
288M ASN* 3.3 7.8 + - - +
289M ALA* 3.1 14.9 + - - +
291M GLN* 1.3 79.5 - - - +
293M ALA* 1.3 58.3 + - - +
295M TRP* 3.2 23.5 + + - +
296M ILE* 3.0 42.2 + - + +
559M LEU* 4.4 18.8 - - + -
589M PHE* 4.2 18.5 - + + -
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Residues in contact with ALA 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M ALA* 3.8 19.0 - - + +
158M LEU* 5.1 1.3 - - + -
289M ALA 2.9 9.6 + - - +
290M ARG* 3.7 5.2 - - - +
292M PHE* 1.3 78.4 - - - +
294M GLU* 1.3 66.2 + - - +
296M ILE* 3.2 7.5 + - - +
297M CYS* 2.9 23.9 + - - +
304M CYS* 4.6 14.0 - - + +
306M VAL* 3.5 32.1 - - + -
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Residues in contact with GLU 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M VAL* 3.9 30.8 - - + +
101M VAL* 4.2 23.3 - - + +
115M ALA* 4.0 10.3 - - + +
290M ARG* 2.9 28.9 + - - +
291M GLN* 3.6 16.7 + - - +
293M ALA* 1.3 75.4 - - - +
295M TRP* 1.3 57.2 + - - +
297M CYS* 3.3 2.1 + - - +
298M HIS* 2.9 32.9 + - - +
592M PHE* 3.4 23.7 - - + -
596M ARG* 3.4 28.2 + - - -
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Residues in contact with TRP 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257M MET* 5.5 2.0 - - + -
267M GLU* 4.1 29.4 - - + -
270M ILE* 3.8 26.9 - - + -
271M ILE* 3.8 15.7 - - + -
291M GLN 2.9 13.8 + - - +
292M PHE* 3.3 23.3 - + - +
293M ALA 3.1 0.2 - - - -
294M GLU* 1.3 74.7 - - - +
296M ILE* 1.3 84.0 + - + +
298M HIS* 3.5 3.8 + - + +
299M LEU* 2.9 35.5 + - + +
587M LYS 2.6 30.2 + - - -
588M SER 2.8 10.0 + - - -
589M PHE* 3.6 28.9 - + + -
592M PHE* 3.5 39.0 - + + -
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Residues in contact with ILE 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156M SER* 5.2 3.8 - - - +
270M ILE* 3.8 24.5 - - + -
279M TYR* 3.8 17.3 - - + +
281M PHE* 3.7 29.2 - - + -
292M PHE* 3.0 34.6 + - + +
293M ALA* 3.2 8.0 + - - +
295M TRP* 1.3 89.6 - - + +
297M CYS* 1.3 57.8 + - - +
299M LEU* 3.7 4.4 - - - +
300M HIS* 2.9 35.0 + - + +
302M GLN* 4.7 5.3 - - + +
304M CYS* 4.7 17.0 - - + -
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Residues in contact with CYS 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M VAL* 4.7 4.7 - - + -
115M ALA 4.1 8.7 - - - +
116M LEU* 3.4 38.8 - - - -
117M PRO* 3.4 13.0 - - - -
293M ALA 2.9 16.6 + - - +
294M GLU* 3.6 7.4 - - - +
296M ILE* 1.3 73.1 - - - +
298M HIS* 1.3 57.1 + - - +
299M LEU 2.9 4.3 + - - -
300M HIS 3.0 0.3 + - - -
301M LYS* 2.5 37.5 + - - -
302M GLN 3.0 27.6 - - - +
304M CYS* 5.3 1.5 - - + +
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Residues in contact with HIS 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M MET 5.3 0.2 - - - -
97M PRO* 3.4 41.0 - - + +
98M ARG* 4.5 10.3 - - + +
99M VAL* 5.4 4.5 - - + +
294M GLU 2.9 20.8 + - - +
295M TRP* 4.1 4.2 - - + +
297M CYS* 1.3 73.7 - - - +
299M LEU* 1.3 59.1 + - - +
301M LYS* 4.2 10.0 + - - +
586M GLU 5.7 3.6 - - - -
587M LYS* 4.3 26.7 + - + +
592M PHE* 4.6 14.2 - + + -
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Residues in contact with LEU 299 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270M ILE* 3.8 23.1 - - + +
271M ILE* 4.0 18.8 - - + +
295M TRP* 2.9 27.9 + - + +
296M ILE* 3.7 4.7 - - - +
298M HIS* 1.3 81.4 - - - +
300M HIS* 1.3 87.5 + - + +
301M LYS* 3.6 1.1 - - - +
583M TYR* 5.1 6.6 + - - +
587M LYS* 3.6 51.2 + - + +
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Residues in contact with HIS 300 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270M ILE 3.3 21.3 + - - -
271M ILE 5.5 0.4 - - - -
273M LEU* 3.6 24.5 + - + -
274M PRO 4.7 2.2 - - - -
275M ASP* 2.6 41.5 - - - +
277M VAL* 4.1 5.6 - - + +
279M TYR* 2.9 41.2 + + - -
296M ILE* 2.9 17.6 + - + +
299M LEU* 1.3 98.8 - - + +
301M LYS* 1.3 67.1 + - - +
302M GLN* 2.9 31.7 + - + +
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Residues in contact with LYS 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M PRO* 3.8 22.1 - - + +
120M GLU* 5.2 3.1 - - - +
275M ASP* 4.4 16.8 - - - +
297M CYS 2.5 20.1 + - - +
298M HIS* 4.8 9.0 - - - +
299M LEU 3.6 1.5 - - - +
300M HIS* 1.3 74.5 - - - +
302M GLN* 1.3 54.4 + - - +
303M PRO* 4.5 1.6 - - - +
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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