Contacts of the helix formed by residues 270 - 282 (chain M) in PDB entry 4G7Z
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 270 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144M PRO* 3.7 13.6 - - - +
165M LEU* 3.7 21.3 - - - +
269M LEU* 1.3 82.2 - - - +
271M GLU* 1.3 59.3 + - - -
272M ALA* 3.1 2.5 - - - -
273M GLY* 3.2 10.3 - - - -
274M ARG* 2.5 33.3 + - - +
288M ARG* 3.9 2.0 - - - +
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Residues in contact with GLU 271 (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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165M LEU* 5.4 1.2 - - - +
270M GLY* 1.3 71.7 - - - -
272M ALA* 1.3 62.4 + - - +
274M ARG* 3.5 28.5 + - - +
275M TYR* 3.2 20.1 + - - +
288M ARG* 3.4 35.3 + - - +
464M LEU* 4.2 10.9 - - + +
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Residues in contact with ALA 272 (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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143M SER* 4.4 4.5 - - - +
144M PRO* 5.2 0.4 - - + -
270M GLY* 4.8 1.8 - - - -
271M GLU* 1.3 79.6 - - - +
273M GLY* 1.3 52.3 + - - +
275M TYR* 2.9 7.5 + - - +
276M LYS* 2.7 38.3 + - - +
332M ARG* 4.0 20.6 - - - +
464M LEU* 3.6 45.3 - - + +
466M PHE* 4.5 5.4 - - + -
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Residues in contact with GLY 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M PRO* 3.1 38.8 + - - +
145M GLY* 3.7 8.4 - - - -
269M LEU* 3.7 12.8 - - - +
270M GLY* 3.1 11.4 + - - -
272M ALA* 1.3 79.8 - - - +
274M ARG* 1.3 59.6 + - - +
276M LYS 3.4 0.2 + - - -
277M ALA* 3.2 18.4 + - - +
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Residues in contact with ARG 274 (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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269M LEU* 3.8 10.9 - - - +
270M GLY 2.5 19.9 + - - +
271M GLU* 3.5 31.9 + - - +
273M GLY* 1.3 73.1 - - - +
275M TYR* 1.3 61.8 + - - +
277M ALA* 3.7 2.6 + - - +
278M GLU* 3.2 33.1 + - - +
284M ARG* 3.1 18.8 - - - +
285M LEU* 2.8 31.7 + - + +
286M SER* 3.8 4.4 + - - +
287M GLY* 3.2 45.1 - - - +
288M ARG* 4.1 14.2 - - + +
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Residues in contact with TYR 275 (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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271M GLU 3.2 10.7 + - - +
272M ALA* 2.9 11.5 + - - +
274M ARG* 1.3 81.5 - - - +
276M LYS* 1.3 74.9 + - + +
278M GLU* 3.1 16.6 + - + +
279M GLU* 2.9 54.4 + - + +
464M LEU* 5.0 14.1 - - + -
466M PHE* 5.0 13.5 - + - -
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Residues in contact with LYS 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M SER* 3.9 7.2 - - - +
144M PRO 3.5 20.6 - - - +
145M GLY* 3.9 4.5 - - - -
146M VAL 4.6 5.8 + - - -
147M TYR* 3.1 39.4 - - - -
272M ALA 2.7 21.2 + - - +
273M GLY 3.4 2.9 + - - +
275M TYR* 1.3 80.3 - - + +
277M ALA* 1.3 57.5 + - - +
279M GLU* 3.5 3.4 + - + +
280M LYS* 3.0 36.2 + - - +
323M ASP* 5.5 0.8 + - - -
329M GLY 3.8 12.8 - - - +
330M ASN* 3.7 15.3 - - - +
466M PHE* 4.0 22.2 - - + -
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Residues in contact with ALA 277 (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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145M GLY* 4.5 1.0 - - - -
146M VAL* 4.2 20.2 - - + +
269M LEU* 5.0 8.3 - - + -
273M GLY 3.2 14.1 + - - +
274M ARG 4.0 3.8 - - - +
276M LYS* 1.3 76.6 - - - +
278M GLU* 1.3 60.8 + - - +
280M LYS* 4.4 2.5 - - - -
281M LEU* 2.9 55.2 + - + +
283M ILE* 4.5 2.6 - - + +
285M LEU* 5.1 9.6 - - + -
302M VAL* 5.6 3.8 - - + -
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Residues in contact with GLU 278 (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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274M ARG* 3.2 31.7 + - - +
275M TYR* 3.1 20.8 + - + +
277M ALA* 1.3 78.7 - - - +
279M GLU* 1.3 56.3 + - - +
282M GLY* 3.0 22.7 + - - -
283M ILE* 3.2 32.7 + - + +
284M ARG* 2.9 37.3 + - - -
285M LEU* 3.2 21.7 + - + +
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Residues in contact with GLU 279 (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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275M TYR* 2.9 46.6 + - + +
276M LYS* 4.0 3.1 - - - +
278M GLU* 1.3 77.5 - - - +
280M LYS* 1.3 69.0 + - - +
282M GLY* 3.7 5.5 + - - -
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Residues in contact with LYS 280 (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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146M VAL 3.6 17.3 - - - +
148M PHE* 3.5 19.7 - - + -
276M LYS* 3.0 24.3 + - - +
277M ALA* 3.8 2.7 - - - +
279M GLU* 1.3 80.8 - - - +
281M LEU* 1.3 68.1 + - + +
309M TYR* 3.1 41.5 + - + +
321M GLU* 3.0 26.9 + - - +
323M ASP* 2.7 39.8 + - - +
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Residues in contact with LEU 281 (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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146M VAL* 4.0 14.4 - - + -
148M PHE* 4.1 4.0 - - + -
277M ALA* 2.9 35.6 + - + +
280M LYS* 1.3 80.3 - - + +
282M GLY* 1.3 62.3 + - - +
283M ILE* 3.5 21.5 - - + +
302M VAL* 4.9 2.2 - - + +
305M PRO* 3.7 19.3 - - + +
306M THR* 3.5 47.6 - - + -
308M ARG* 3.1 22.7 + - - +
309M TYR* 4.0 14.8 - - + -
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Residues in contact with GLY 282 (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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278M GLU 3.0 13.8 + - - -
279M GLU 3.7 4.4 + - - -
280M LYS 3.4 3.2 + - - -
281M LEU* 1.3 79.6 - - - +
283M ILE* 1.3 61.9 + - - +
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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